US EPACompTox Chemicals Dashboard
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Center for Computotionol Toxicology and Exposure, U.S. Environmentol Protection Agency, RTP, NC
The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA
Globol Marine Summit 2019
UNCW, Wilmington, NC

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A little bit about me...
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NMR spectroscopist by training
MUiW	Antony WllNwm and lOrfl BJinov
Contemporary Computer-Assisted
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Elucidation
RSC Publishing
lecture Note in Chemistry 89
Mikhail E. Elyashberg
Antony J.Williams
The Art of Solving Problems
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Modern NMR
Approaches to the
Structure Elucidation of
Natural Products
Volume 2 Daia Acqoistton and Appi
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Type-ahead Search
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(s A -A


Product/Use Categories Assay/Gene
PSZZj


emodin)

Emodin
DTXSID5Q25231

j566.
Emodin anthrone
DTXSID80197684

~,v
Emodin-8-o-beta-gentiobioside
DTXSID20216681

j6J6^
Emodin 3-methyl ether
DTX5ID2Q200101


emodin-8-methyl ether
DTXSID30191177

.c6i.
Emodinanthrone
DTXSIDS0197684

9V
Emodine
DTXSID2030695
8

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Substring Search: Enniatin (10/29)
Chemicals
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Enniatin
' Identifier substring search
Search Results
Searched with 'Synonym Substring': Enniatin
DTXSID X I CASRN X I TOXCAST X I
-o
Enniatin B1
DTXSID:DTXSID70891861
CASRN:19914-20-6
TOXCAST:-
Enniatin B2
DTXSID:DTXSID501017635
CASRN:632-91-7
TOXCAST:-
O
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Enniatin B
DTXSID:DTXSID30891862
CASRN:917-13-5
TOXCAST:-
Enniatin F
DTXSID:DTXSID601017690
CASRN:144446-20-8
TOXCAST:-
oc;
CM, H
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Enniatin A
DTXSID:DTXStD90891863
CASRN:2503-13-1
TOXCAST:-
HC CH, CHj IV CH,
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Enniatin B4
DTXSI D:DTXSID601017783
CASRN: 19893-21-1
TOXCAST:-
yis
Enniatin A1
DTXSID:DTXSID50891864
CASRN:4530-21 -6
TOXCAST:-

HiC
Enniatin K1
DTXSID:DTXSID801017977
CASRN:716318-00-2
TOXCAST:-
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Enniatin J1
DTXSID:DTXSID701017631
CASRN:19893-15-3
TOXCAST:-


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Enniatin B3
DTXSID.DTXSI D401017632
CASRN:864-99-3
TOXCAST:-
9

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Chemical Details Page
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Environmental Protection Home Advanced Search Batch Search Lists v Predictions Downloads
Agency
Emodin
518-82-1 | DTXSID5025231
Searched by DSSTox Substance Id.
EXECUTIVE SUMMARY
PROPERTIES
ENV. FATE/TRANSPORT
HAZARD
ADME
~	EXPOSURE
~	BIOACTIVITY
SIMILAR COMPOUNDS
GENRA (BETA)
RELATED SUBSTANCES
SYNONYMS
~	LITERATURE
LINKS
10

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Experimental & Predicted Properties
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DETAILS
EXECUTIVE SUMMARY
PROPERTIES
ENV. FATE/TRANSPORT
HAZARD
ADME
~	EXPOSURE
~	BIOACTIVITY
SIMILAR COMPOUNDS
GENRA (BETA)
RELATED SUBSTANCES
SYNONYMS
Property
Summary
Download
Columns
Property *
Experimental average '
Predicted average JV
LogPi Octanol-Water
-
3.59 1
Melting Point
255 (5)
250 \
Boiling Point
587 (1)
453 i
Water Solubility
-
1.13e-4 W
Vapor Pressure
-
2.28e-10 J
Flash Point
-
302 &
Surface Tension
-
85.4 #
Index of Refraction
-
1.75 f
Molar Refractivity
-
69.1 M
uPoJarizabilitY .
^ A
i j i
11

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Open Source Prediction Models
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Model Results
Predicted value: 2.59
Global applicability domain: |Inside)
Local applicability domain index: 0.548
Confidence level: 0.695
Model Performance
5-fold CV (75%)
Training (75%)
Test (25%)
Q2
RMSE
R2
RMSE
R2
RMSE
0.850
0.690
0.860
0.670
0.860
0.780
Nearest Neighbors from the Training Set
I £-

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OPERA Predicted Properties
An automated curation procedure for addressing
chemical errors and inconsistencies in public
datasets used in QSAR modelling
K. Mansouri, C. M. Grulke, A. M. Richard, R. S. judsori & A. J. Williams
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To cite this article: K. M\
A	,	,	sv Mansouri et aL JCheminform (20131 I0:!0
An automated curation pr https://doi.org/10.1 ise/si3321-018-0263-1
datasets used in QSAR n
DPI: 10.1 Q8Q/1Q62936X.:
To link to this article: h
RESEARCH ARTICLE
0 Journal of Chemlnformatics
Open Access
Crow Mark
OPERA models for predicting	®
physicochemical properties and environmental
fate endpoints
Kamel Mansouri1,2,3*1Q>, Chris M. Grulke1, Richard S. Judson and Antony J. Williams'
OPERA Models: https://qithub.com/kmansouri/OPERA
13

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*	Toxicologies! properties
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Oral rat LD50
*	Bioaccumulation factor
^ Developmental toxicity
*	Ames mutagenicity
*	Estrogen Receptor RBA
^ Estrogen Receptor Binding
*	Physical properties
S Normal boiling point
® Melting point
^ Flash point
*	Vapor pressure
*	Density
Surface tension
*	Thermal conductivity
^ Viscosity
Water solubility

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Chemicals
MAE*
Entire set
0.43
Similarity coefficient > 0.5
0.66
*Mean absolute error in -LoglO(rnol/kg)

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A
Subtype w
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A
Value *
Units »
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Source »
fe
5
LR50

repeat dose
1873
g/ha
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predatory mite
EFSA OpenFoodTox
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5
LR50
-
repeat dose
1873
g/ha
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-
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EFSA OpenFoodTox
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5
LD50
-
subacute
100
mg/kg
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fe
5
LD50
-
acute
2000
mg/kg
acute
oral
bobwhite quail
EFSA OpenFoodTox
EFSA
fe
5
LD50
-
acute
100
ug/piece
acute
oral
honey bee
EFSA OpenFoodTox
EFSA















fe
5
LD5

LUbU: I he dose ot a toxicant or microbe that will kill bU percent ot the test organisms within a designated period. I he
lower the LD50, the more toxic the compound.
EFSA OpenFoodTox
EFSA
6 records
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Hazard Data from "ToxVal DB"
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• ToxVal Database contains following data
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-~30 sources of data
-~22,000 sub-sources
—-5000 journals cited
-~70,000 literature citations

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In Vitro Bioassay Screening
ToxCast and Tox21
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Chemical Activity Summary^
©TOXCAST DATA
O ASSAY DETAILS
nuclear receptor
ceil cycle
background measurement
cell morphology
DNA binding
hydrolase
L5-
L0-
5.5-
5.0-
4.5-
40-
3.5
3.0-
2.5-
2.0-
1.5-
1.0-
®
c
4
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• *
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% .
», o
.ll •
i-*
AC50 (uM)

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In Vitro Bioassay Screening
ToxCast and Tox21
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A Download ~ Columns v 10
123 active of 402 assays
Search query
Show Inactive CD Show Background
Name *
Gene Name ~
Gene Url
Hit
Call -
AC50
A
logAC50
A.
Cutoff
~
ModlAcb
A
Intended
Target
Family »
© ACEA_ER_80hr
estrogen receptor 1
https://www.ncbi.nlm.nih.gov/gene/2099
ACTIVE
0.544
-0.265
26.9
-0.387
nuclear
receptor
© ATG_ERE_CIS_up
estrogen receptor 1
https://www.ncbi.nlm.nih.gov/gene/2099
ACTIVE
0.623
-0.206
0.503
-0.570
nuclear
receptor
O TOX21_MMP_rhodamine

-
ACTIVE
0.659
-0.181
44.6
-0.626
background
measurement
O ATG_ERa_TRANS_up
estrogen receptor 1
https://www.ncbi.nlm.nih.gov/gene/2099
ACTIVE
0.670
-0.174
1.13
-0.235
nuclear
receptor
O TOX21_MMP_ratio_down

-
ACTIVE
0.713
-0.147
38.7
-0.708
cell
morphology
O TOX21_HDAC_lnhibition

-
ACTIVE
2.07
0.315
20.0
-0.634
hydrolase
e
TOX21_E Ra_ LU C_V M 7_Ag o n i st
estrogen receptor 1
https://www.ncbi.nlm.nih.gov/gene/2099
ACTIVE
3.04
0.483
20.0
3,00e-2
nuclear
receptor
19

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Identifiers to Support Sea
Synonym
Emodin
1,3,8-Trihydroxy-6-methylanthracene-9,10-dione
9,10-Anthracenedione, 1,3,8-trihydroxy-6-methyl-
518-82-1 |
9,10-Anthracenedione, l,3,8-trihydroxy-6-methyl-
Active CAS-RN
1,3,8-trihidroxi-6-metilantraquinona
l,3,8-Trihydroxy-6-methyl-9,10-anthraquinone
l,3,8-Trihydroxy-6-methylanthrachinon
1,3,8-trihydroxy-6-methylanthraquinone
l,6,8-Trihydroxy-3-methylanthraquinone
3-Methyl-T,6,8-trihydroxyanthraquinone
4,5,7-Trihydroxy-2-methylanthraquinone
Anthraquinone, l,3,8-trihydroxy-6-methyl-
Frangula emodin
Frangulic acid
NSC 408120
v»EPA
United S«las
Erwf#onmont»1 Protection
Agamcy
* Quality
Valid
Valid
Valid
Valid
Good
Good
Good
Good
Good
Good
Good
Good
Good
Good
Good
Good
20

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Built in	"M
21

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Emodin
518-82-1 | DTXSID5025231
Searched by Approved Name.
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1) Select PubMed starting point query then 2) click on Retrieve. ©
Select a Query Term
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Female Reproduction
GeneTox
Cancer
Clinical Trials
Embryo and embryonic development
Child (infant through adolescent)
Dust and Exposure
Food and Exposure
Water and Exposure
Algae
Disaster / Emergency

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Literature Searching
Abstract Sifter
1) Select PubMed starting point query then 2) click on
Retrieve. ©
Cancer v
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~

Hazard


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Metabolism/PK/PD


Chemical Properties


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Androgen Disruption


Female Reproduction


GeneTox


Cancer


Clinical Trials


Embryo and embryonic development


Child (infant through adolescent)


Dust and Exposure


Food and Exposure


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Alaae


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Literature Searching
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Abstract Sifter
1) Select PubMed starting point query then 2) click on Retrieve. ©
Cancer	v	©
568 of 568 articles loaded-.
Optionally, edit the query before retrieving.
To find articles quickly, enter terms to sift abstracts. 0

PMID
Year
Title Authors Journal R<
Rev
~
31572001
2019
Emodin sensitizes human pancreatic cancer cells to EGFR inhibitor through s...
Wang; Chen; Chen; Hong; Liao; Zhang; Tong
Cancer management and research

~
31524243
2019
Emodin: Its role in prostate cancer-associated inflammation (Review).
Tu; Wu; Tan; Yang; Fang
Oncology reports

Q
31462111
2019
Combination of targeted daunorubicin liposomes and targeted emodin liposo...
Fu; Tang; Liu; Gong; Kong; Yao; Jing; Cai; Li; Ju
Journal of drug targeting

~
31424332
2019
Components synergy between stilbenes and emodin derivatives contributes to..
Zhang; Liu; Tu; Li; Song; Zhu; Zhou; Wang; Li; Xiao...
Xenobiotica; the fate of foreign compounds in biolo...

~
31420258
2019
Anthraquinones and autophagy - Three rings to rule them all?
Deitersen; El-Kashef; Proksch; Stork
Bioorganic & medicinal chemistry
y
~
31349435
2019
Effect of structure in ionised albumin based nanoparticle: Characterisation, E..
Siri; Ruocco; Achilli; Pizzuto; Delgado; Ruysschaert..
Materials science & engineering. C, Materials for bi..

~
31325728
2019
Anticancer activity of emodin is associated with downregulation of CD 155.
Fang; Zhao; Iwanowycz; Wang; Yin; Wang; Fan
International immunopharmacology

~
31308025
2019
p-Dihydroartemisinin-Emodin Promotes Apoptosis by Activating Extrinsic and I...
Li; Gao; Yang; Jin; Sun
Annals of clinical and laboratory science

~
31294125
2019
Pharmacological properties of Rheum turkestanicum Janisch.
Ghorbani; Amiri; Hosseini
Heliyon
y
~
31288005
2019
Emodin suppresses growth and invasion of colorectal cancer cells by inhibitin
Dai; Ding; Cao; Xu; He; Liu; Ju
European journal of pharmacology

~
31280208
2019
Peroxiredoxin V Inhibits Emodin-induced Gastric Cancer Cell Apoptosis via th...
Jin; Sun; Liu; Lee: Kim; Kim; Jiao; Han; Jin; Shen; L...
In vivo (Athens, Greece)

~
31236404
2019
Anticancer Effects of Emodin on HepG2 Cell: Evidence from Bioinformatic An...
Zhou; Wang; Sun; Ye; Liu; Zhou; Tang
BioMed research international

~
31234244
2019
Emodin, as a mitochondrial uncoupler induces strong decreases in adenosine..
Sugiyama; Shudo; Hosokawa; Watanabe; Nakano; ...
Genes to cells : devoted to molecular & cellular me..

~
31190872
2019
Anti-tumor effect of aloe-emodin on cervical cancer cells was associated with ...
Gao; Wu; Huang; Wang; Li; Xu; Ran
OncoTargets and therapy

~
31128032
2019
Aloe emodin exerts potent anticancer effects in MIAPaCa-2 and PANC-1 hum...
Du; Zhang; Tao; Wang; Yan; Zhang; Huang
Journal ofB.U.ON. : official journal of the Balkan U..

~
31114158
2019
Emodin enhances antitumor effect of paclitaxel on human non-small-cell lung ...
Chen; Zhang; Zhang
Drug design, development and therapy

24

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Sifting retrieved articles
A EPA
Unitad S:ales
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To find articles quickly, enter terms to sift abstracts. 0
emodin	anti-tumor	gynecol
To find articles quickly, enter terms to sift abstracts. 0
emodin	anti-tumor
Clear Terms
Download / Send to...
Download Sifter for Excel

D
emodin
anti-tumor I
gynecol
Total
PMID
Year
Title
Authors
Journal
Rev
~
1
B
7
4
0
11
22474959
2012
Synthesis and anti-tumor activity evaluation of rhein...
Yuan; Hu; He; Deng
Natural product communications

O
0
3
0
3
28922732
2017
Physcion 8-O-p-glucopyranosideregulates cell cycl..
Li; Li; Zhu; Song
Biomedicine & pharmacotherapy = Biomedecine &

O
0
3
0
3
28570979
2017
Physcion 8-O-p-glucopyranoside suppresses tumor...
Wang; Jiang; Guo; Lv; Liu; Wei; Ming; Tian
Biomedicine & pharmacotherapy = Biomedecine & ...


























a
13
3
6
22
26162964
2015
Anti-tumor effect of emodin on gynecological cance...
Wang. Yu; Zhang; Ge; Gao; Zhang; Lou
Cellular oncology (Dordrecht)



















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~
p
3
2
0
5
27062805
2016
[Research progress in anti-tumor effect of emodin].
Lin; Wang; Ling
Zhongguo Zhong yao za zhi = Zhongguo zhongyao
Y
~
0
2
0
2
26144377
2015
Physcion induces mitochondria-driven apoptosis in .
Chen; Gao; Han; Ye; Xie; Wang
European journal of pharmacology

~
7
2
0
9
22876305
2012
Antitumor activity of emodin against pancreatic can..
Lin; Wei; Chen; Chen; Tong; Wang; Ni; Liu; Guo; Liu
PloS one

Q
12
2
0
14
19857484
2009
Anti-tumor activity of emodin against human chroni. ..
Chun-Guang, Jun-Qing; Bei-Zhong; Dan-Ting; Cho.
European journal of pharmacology

~
8
1
0
9
31190872
2019
Anti-tumor effect of aloe-emodin on cervical cancer...
Gao; Wu; Huang: Wang; Li; Xu; Ran
OncoTargets and therapy

a
6
1
0
7
30832378
2019
Design and Synthesis of Novel Anti-Proliferative E...
Yang; Jin; Quan: Piao
Molecules (Basel, Switzerland)

0
8
1
0
9
30648710
2019
Magnetic liposomal emodin composite with enhanc...
Song; Sheng: Xu; Dong: Xu; Li; Wang: Wu; Yang; S...
Biomaterials science

~
2
1
0
3
30199885
2018
Aloe-Emodin Induces Endoplasmic Reticulum Stres..
Cheng; Dong
Medical science monitor: international medical jour..

~
0
1
0
1
28810515
2017
Physcion blocks cell cycle and induces apoptosis in..
Gao: Liu; Guo, Bai; Yang; Chen
Biomedicine & pharmacotherapy = Biomedecine & ...

D
5
1
0
6
28669313
2017
Dose-dependent role of novel agents emodin and B...
Braumann; Koplin; Geier; Hohn; Pohlenz; Dubiel; R...
Acta chirurgica Belgica

Anti-tumor effect of emodin on gynecological cancer cells.
PURPOSE: Although an anti-tumor effect of emodin has been reported before, its effect on human gynecllogical cancer cells has so far not been studied. Here, we assessed the effect of emodin on cervical cancer-derived (Hela). choriocarcinoma-
derived (JAR) and ovarian cancer-derived (HO-8910) cells, and investigated the possible underlying molecular and cellular mechanisms.
METHODS AND RESULTS: The respective cells were treated with 0, 5,10 or 15 pM emodin for 72 h. Subsequently, MTT and Transwell in vitro migration assays revealed that emodin significantly decreased the viability and invasive capacity of the
gynecological cancer-derived cells tested. We found that emodin induced apoptosis and significantly decreased mitochondrial membrane potential and ATP release in these cells. We also found that emodin may exert its apoptotic effects via regulating
the activity of caspase-9 and the expression of cleaved-caspase-3. Moreover, we found that emodin induced a cell cycle arrest at the G0/G1 phase, possibly through down-regulating the key ceil cycle regulators Cyclin D and Cyclin E. Interestingly,
emodin also led to autophagic cell death, as revealed by increased MAP LC3 expression, a marker of the autophagosome, and decreased expression of the autophagy regulators Beclin-1 and Atg12-Atg5. Finally, we found that the protein levels of
both VEGF and VEGFR-2 were significantly decreased in emodift-treated ceils, suggesting an anti-angiogenic effect of emodin on gynecological cancer-derived cells.
25

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Cell Oncol (Dordrl 2015 Oct;38(5):353-63. doi: 10.1007/s13402-015-0234-8. Epub 2015 Jul 11
Anti-tumor effect of emodin on gynecological cancer cells.
Wana Y1. Yu H2. Zhang J3. Ge X4. Gao J1. Zhang Y1. Lou G5.
- Author information
1	Department of Gynaecology, Harbin Medical University Cancer Hospital, 150 Hapin Road, Harbin, 150081, China.
2	Cardiopulmonary Function Room, Harbin Medical University Cancer Hospital, Harbin, China.
3	Department of Gynaecology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China.
4	Department of General Surgery, The Provincial Hospital of Heilongjiang, Harbin, China.
5	Department of Gynaecology, Harbin Medical University Cancer Hospital, 150 Hapin Road, Harbin, 150081, China. Gexincom@163.com.
Abstract
PURPOSE: Although an anti-tumor effect of emodin has been reported before, its effect on human gynecological cancer cells has so far not
been studied. Here, we assessed the effect of emodin on cervical cancer-derived (Hela), choriocarcinoma-derived (JAR) and ovarian cancer-
derived (HO-8910) cells, and investigated the possible underlying molecular and cellular mechanisms.
METHODS AND RESULTS: The respective cells were treated with 0, 5,10 or 15 pM emodin for 72 h. Subsequently, MTT and Transwell in
vitro migration assays revealed that emodin significantly decreased the viability and invasive capacity of the gynecological cancer-derived
cells tested. We found that emodin induced apoptosis and significantly decreased mitochondrial membrane potential and ATP release in
26

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Emodin
518-82-1 I DTXSID5025231
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Wikipedia
Emodin 16-methyl-1,3,8-trihydroxyanthraquinone) is a chemical compound that can b|
japonica syn. Polygonum cuspidatum). It is also produced by many species of fungi, incl J(
alia. The common name is derived from Rheum emodi, a taxonomic synonym of Rheum |
ft Average Mass: 270.24 g/mol [ad Isotope Mass Distribution
ft Monoisotopic Mass: 270.052823 g/mol
Read more
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DTXSID:DTXSID6022391
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3',4'.7-Trihydroxyisofiavone
CASRN:485-63-2
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Aloe-emodin
CASRN:481 -72-1
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Anthraquinone. 1,3-dihydroxy-2-methox...
CASRN:10383-63-8
DTXSI D:DTXSI D70146080
Mono.Mass.270.052823
1.8-Dihydroxy-4-hydroxymethylanthraq...
CASRN:128341-04-8
DTXSID:DTXSID70155854
Mono.Mass:270.052823
4',6.7-Trihydroxyisoflavone
CASRN:17817-31-1
DTXSID:DTXSID8022452
Mono.Mass:270.052823
Rubilactone
CASRN:142182-54-5
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Mono.Mass:270.052823
30

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Google "RHMXXJGYXNZAPX-UHFFFAOYSA-N"	J,
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0H National Institutes of Health (.gov) > nlm > chem > chemidplus ~
RHMXXJGYXNZAPX-UHFFFAOYSA-N - Emodin - ChemlDplus
518-82-1 - RHMXXJGYXNZAPX-UHFFFAOYSA-N - Emodin - Similar structures search, synonyms,
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120667-83-6 - RHMXXJGYXNZAPX ... - ChemlDplus
120667-83-6 - RHMXXJGYXNZAPX-UHFFFAOYSA-N - Embodin - Similar structures search,
synonyms, formulas, resource links, and other chemical...
European Bioinformatics Institute >... > CHEMBL289277
ChEMBL - Compound Report Card
... InChl, lnChl=1 S/C15H1 GO5/c1-6-2-8-12(10(17)3-6)15(20)13-9(14(8)19)4... Download InChl.
Standard InChl Key, RHMXXJGYXNZAPX-UHFFFAOYSA-N ...
» National Institute of Standards and Technology (.gov) > webbook > cgi T
Information from the InChl - the NIST WebBook
IUPAC Standard InChlKey: RHMXXJGYXNZAPX-UHFFFAOYSA-N; Connectivity: Structure image
derived from InChl string; 2-d Mol File from the identifier...

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9(10H)-Anthracenone, 1,3-dihydroxy-
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1,3-Bis[(2H)hydroxy]anthracene-9,10-dio...
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Emodin
DTXSID:DTXSID5025231
CASRN:518-82-1
TOXCAST:123/402
2-Hydroxychrysophanol
DTXSI D:DTXSI D70207049
CASRN:58322-78-4
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Questin
DTXS1D:DTXSID30191177
CASRN:3774-64-9
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Aloe emodin anthrone
DTXSID:DTXSID20211510
C ASRN:6247-99-0
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Transformation Product
omega-Hydroxyemodin
DTXSI D:DTXSID60197420
CASRN:481-73-2
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Transformation Product
l I
Emodin anthrone
DTXSID:DTXSID80197684
CASRN:491 -60-1
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Physcione
DTXSID:DTXSID20200101
CASRN:521-61-9
TOXCAST:-
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Archin | Emodin, Frangula | Emodin, Rheum | Frangula Emodin | Frangulic Acid | Rheum Emodir
518-82-1
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Purgative anthraquinone found in several plants, especially Rhamnus frangula. It was formerly u
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CASRN: 163648-25-7
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Mono.Mass: 1142.479002
45

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Maitotoxin (or MTX) is an extremely potent toxin produced by Gambierdiscus toxicus, a dinoflagellate species. Maitotoxin is so potent that it has
been demonstrated that an intraperitoneal injection of 130 rig/leg was lethal in mice. Maitotoxin was named from the ciguateric fish Ctenochaetus
striatus—called "maito" in Tahiti—from which maitotoxin was isolated for the first time. It was later shown that maitotoxin is actually produced by the
dinoflagellate Gambierdiscus
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C Average Mass: 3425.88 g/mol \M Isotope Mass Distribution
Pi Monoisotopic Mass: 3423.581083 g/mol
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ELSEVIER
J1 Review
Keynote
Drug Discovery Today
Volume 17, Issues 13-14, July 2012, Pages 685-701
• r

Towards a gold standard: elsevier
quality in public domain
Drug Discovery Today
Volume 16, Issues 17-18, September 2011, Psges 747-750
Editorial
database's and armrnarhp*
tiie Machines first, humans second: on the importance
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Antony J.
0 Show i
https://d<
data
Alex M Clark i&, Antony J Williams and Sean Ekins
Journal o f Cheminforma tics 2015 7:9
https://doi.org/10.1186/si 3321 -015-0057-7 © Clark et al_; licensee Springer. 2015
Received: 24 November 2014 Accepted: 23 February 2015 Published: 22 March 2015
ind content
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R D aminQmethyiere'iarrt nGlpropyl'i-8-
=obut/l-tS-i:6-methox,t'-3.5-dirne-fr,Y-7-
I SR. 8S. 11R125.1SS. 18S. 19S.22RV 15-
''3-Carbamimiflamidoproav' i-3-isob_tyl-
i 8-171 E.55.6Sh6-metho:cv--3. 5-cimethvl-
1 S-i'S-CarfaamimicamidoproDvli-S-
isobutyvi &-[!' 1 E.3E j-6-methcacy-3.5-
dimethvl-7-phervM .3-hectac en-1 -
¦m
fSR.SR. 11R. 1.2S. 15S-1 3S.22R:-15-:3-
Ca rpami n d a m i c o q*q py I s8-i sc-5 utv-13-
'':lE,3E.5R.6R;h6-T>ethoxv'-3.5-dimethvl-
Search Hits Limit:

15R.SS. 11R. 12-5.15S. 1 SR. 19S.22R -15-
f3-CarbamnYdamidopropvr--B-isQbutyl-
1 S-f; 1 E.3 E. 5S-5S:i-&-rne"thoxv-3.5-
D amino-N-t'3-
(l'5R3S, 11 P. 12S.15S. 1SS.19S.22Rh 11.2:
dicarboxv-S-isooutyl-l 8-
100
¦ • •
• * •
(5R,3S.15S'M5-(3-
f! PamiromethyleneteminQlproDvll-S-
sobutyl-t 8-f l" 1 E.3E. 5S.6Sh6-methoxv-
49

-------
Comparing ChemSpider Structures
A EPA
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HNw-
NH
ChemSpiderlD
Standard InChlKey Stereolayer
WIKIPEDIA
t28-,29-,30-J31+l34-,35-,36'+,37+,38-J40+
CompTox
t28-,29-,30-,31+,34-,35-,36+,37+,38-J40+
4941647
t28-,29-,30-,31+l34-,35-,36+,37+,38-,40+
393078
t28-,29-,30-,31+,34-,35-,36+,37-,38-,40+
57618348
t28-,29-,30-,31+,34-,35-,36+,37-,38-,40+
29342071
t28-,29-,30-,31+,34+,35-/36+,37-,38-,40+
7987594
t28-,29?, 30?, 31+, 34?,35-,36?,37-,38-,40?
22900854
t28-,29?#30+,31-,34+,35+,36-,37-,38-,40-
19692240
NONE
2831283
NONE

-------
C^emSpiderlD
IriChlKey
# Stereocenters
# Different
WIK1PEDIA
ZYZCGG RZIN LQB L-J CG NTXOTSA- N
10/10
0
CompTox
ZYZCGG RZINLQB L-J CG NTXOTSA- N
10/10
0
4941647
ZYZCGG RZI NLQB L-J CG NTXOTSA- N
10/10
0
393078
ZYZCGG RZI NLQBL-GWRQVWKTSA-N
10/10
1
57618348
ZYZCGG RZI N LQB L- U P PCH H EJ SA- N
10/10
1
29342071
ZYZCGG RZI NILQBL- IIJTUTQBSA-N
10/10
2
7987594
ZYZCG G RZ 1N LQB L- B E S LYTP ASA- N
5/10
6
22900854
ZYZCG G RZIN LQB L- QAXS DTKVSA-N
9/10
8
19692240
ZYZCGG RZI N LQB L-ORZJCNCZSA- N
0/10
10
2831283
ZYZCGG RZI N LQB L- U H FFFAOYSA- N
0/10
10

-------
Other Searches
Pub(g)hem About
SEARCH FOR
ZYZCGGRZINLQBL
Treating this q jery as a text search,
Compounds
(17)
UrjjQbsjrj
Show All t entries
CMR.
Query
InChl...
srcjd
Source

src_compoundJd
malches...
1
ChEMBL
CHEMBL444092
. malches...
4
Guide to
Pharmacology
4735
matches...
6
KEGG Ligand
CQ5371
. malches. .
7
ChEBI

6925
. matches. .
9
ZINC

ZIN COO 0169715525
malches...
9
ZINC

ZIN C00025523S110
matches...
9
ZINC

ZIN COO 0255233111
.matches...
9
ZINC

ZIN COO 025523-3112
matches. .
9
ZINC

ZIN CO 00255233113
malches...
9
ZINC

ZINC0002552S3114
malches...
9
ZINC

Zl N CO 0 0255233115
malches
9
ZINC

Zl N CO 0 0 533653042
matches...
9
ZINC

ZIN CO0066963040 3
...malches...
10
eMolecules
26754757
. malches...
10
eMolecules
31239828
-malches...
11
IBM Patent
System
DA3C2F25F29692734272194E DOE2C009
malches...
14
FDA SRS
EQ3332342Y






-------
Delivering a Better Database
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An ideal database would provide:
- Curated CAS Number-Name mappings with "correct"
chemical structures
We have full time curators checking data
b
Record Information	T
1Tb Citation: U.S. Environmental Protection Agency. Chemistry Dashboard,
httpsv'/cornptox.epa.gov/dashboard/DTXSID303165^ (accessed Mar 17th, 201S). Microcystin LR
Data Quality:
i	—									1
{ Level 1: Expert curated, highest confidence in accuracy and consistency of unique chemical 'dentifiers	{
i												i
Leve 2; Expert curated, unique chemical dentifiers using multiple sources
Leve 3: Program m at? cally curated from h:gh quality EPA source, unique chemical identifiers have no conflicts in ChemID and
PubChem
Leve 4; Programmat'caily cjraied from ChemID, unique chemical identifiers have no conflicts n PubChem
Leve 5: Programmatically curated from ACToR or PubChem, unique chemoal dentifiers with low confidence, single public source
53

-------
Substance Mapping

1
(1 of 66) ' <-*
1 2 3 4 5
6 ^ 7 | 8 ][ 9 ][ 10 P( » )[ ~' 25 t f


Source Casm
Source Name
Hit Substance_ID
Hit Casrn
Hit Name

B
¦	 II
o
19398-89-1
4-Decene
DTXSID50876156
19689-18-0
4-Decene

Remove
Validation

o
112926-00-8
silica gel, cryst. -
free
DTXSID9029851
112926-00-8
Hydrated silica

Remove
Validation

o
124-28-7
1-
Octadecanamine,
N,N-dimethyl-
DTXSID4027026
124-28-7
N,N-Dimethyl-1-
octadecanamine



o
1330-43-4
Boron sodium
oxide
DTXSID2034388
1330-43-4
Sodium
tetraborate

Remove
Validation

o
13492-26-7
Mono- and di-
potassium salts
of phosphorous
acid
DTXSID9035961
13492-26-7
Phosphonic acid,
potassium salt
(1:2)

Remove
Validation

o
135-37-5
Glycine, N-
(carboxymethyl)-
N-(2-
hydroxyethyl)-,
disodium salt
DTXSID804200S
135-37-5
Ethanoldiglycine
disodium salt

Remove



-------
Subtleties
v>EPA
Unitad S'Blos
Ewwonmont*! Protection
*a«ocY
"4-Decene"
H^C.
H-,C
CH-
19398-89-1
19689-18-0
E/Z-stereochemistry
E-stereochemistry
55

-------
Crowdsourced Curation
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New Comment
Comment
Describe the issue you're seeing here,.
Email address
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~
I m not *
Show 25 ~
Dexamethadone sodium phosphate
Submit Con-rant
Crowdsourced Comments
Sort Qpfcons: original order t date chemical status
This didn't show up when I searched for dexamethasone onfy when I speoficaiiy
socked wlh the CAS number.
CHEMBL2311179
Change preferred name to B. 1 Q-Dehyd ro-1 0-nortestosterane (or alternative}. See
IntipsjVpubchem.rK&i.nlm.nih.govi'compound/11747706
1-(4-CARBAMOYLPHEf'4YL>3-METI-ri'L-3- ..
I
OH
DTXCID601033319 associated wth this record has no InChlKey despite SMILES and
InOil fields. Change preferred name to" 1 -(4-CarbamoyIpneny1>3-n"fithy^3-
hydroxytriazene" {remove caps)

-------
Uflitod Stains
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57

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Batch Searching
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Singleton searches are useful but people
generally want data on LOTS of chemicals!
• Typical questions
-	What is the list of chemicals for the formula CxHyOz
-	What is the list of chemicals for a mass +/- error
-	Can I get chemical lists in Excel files? In SDF files?
-	Can I include properties in the download file?
58

-------
Batch searching
v>EPA
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JOURNAL
O F
AGRICULTURAL and
FOOD CHEMISTRY
Review
pubsacs.org/JAFC
Emerging Mycotoxins: Beyond Traditionally Determined Food
Contaminants
>»T
Chris tiane Gruber-Dorninger, Barbara Novak/ Veronika Nagl, and Franz Berthiller*'
BIOM1N Research Center, Technopark 1, 3430 Tulln, Austria
Christian Doppler Laboratory for Mycotoxin MetaboUsm and Center for Analytical Chemistry, Department of Agrobiotechnology
(IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
59

-------
Public release had 16/17
mycotoxinsAast one registere
v»EPA
United Stales
Erwf#onmont»1 Protection
Ao**ky

A
B
C
D
1
INPUT
FOUND BY
DTXSID
PREFERRED NAME
2
enniatin A
Approved Name
DTXSID90891863
Enniatin A
3
eriniatin B
Approved Name
DTXSID30891862
Enniatin B
4
enniatin A1
Approved Name
DTXSID50891864
Enniatin A1
5
enniatin B1
Approved Name
DTXSID70891861
Enniatin B1
6
beauvericin
Approved Name
DTXSID00891834
Beauvericin
7
moniliformin
Approved Name
DTXSID10185731
Moniliformin
8
fusaproliferin
NO MATCH
-
-
9
fusaric acid
Approved Name
DTXSID5023085
Fusaric acid
10
culmorin
Approved Name
DTXSID10891805
Culmorin
11
butenolide
Synonym
DTXSID7075422
2(5H)-Furanone
12
sterigmatocystin
Approved Name
DTXSID2021280
Sterigmatocystin
13
emodin
Approved Name
DTXSID5025231
Emodin
14
mycophenolic acid
Approved Name
DTXSID4041070
Mycophenolic acid
15
alternariol
Approved Name
DTXSID80214305
Alternariol
16
alternariol monomethyl ether
Approved Name
DTXSID30178004
Alternariol monomethyl ether
17
tenuazonic acid
Approved Name
DTXSID30893265
Tenuazonic acid
60

-------
Add Other Data of Interest
v>EPA
Unitad S'Blos
Ewwonmont*! Protection
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Intrinsic And Predicted Properties
® Molecular Formula O
* Average Mass
D Monoisotopic Mass 0
U TEST Model Predictions
OPERA Model Predictions O
Metadata
f DTXSID PREFERRE
molecul; average
TOXVAL D
TOXCAST
TOXCAST
PUBCHEM
WIKIPEDIA
ARTICLE
; DTXSID90Enniatin A
C36H63N3C
681.912
Y
-
-
-
-

; DTXSID30Enniatin B
C33H57N3C
639.831
Y
-
-
-
-
; DTXSI D5Q Enniatin A1
C35H61N3C
667.885
Y
-
-
-
-

iDTXSID70 Enniatin B1
C34H59N3C
653.858
Y
-
-
-
-

; DTXSIDOO Beauvericin
C45H57N3C
783.963
Y
-
-
-
i DTXSID10 Moniliformin
C4H203
98.057
Y
-
-
37
Y

: DTXSIDOCTerpestacin
C27H40O5
444.612
-
-
-
-
; DTXSIDSOFusaric acid
C10H13NO;
179.219
Y
r1.27
1/79
115
Y

; DTXSIDICCulmorin
C15H2602
238.371
-
-
-
-
-

; DTXSID4C Butenolide
C6H7N03
141.126
-
-
-
-
-

; DTXSID2C Sterigmatoc
C18H1206
324.288
Y
-
-
23
Y

iDTXSIDSOEmodin
C15H10O5
270.24
Y
r30.6
123/402
194
Y

i DTXSID4C Mycophenol
C17H20O6
320.341
Y
r22.55
53/235
181
Y

; DTXSI D8C Alternariol
C14H10O5
258.229
-
-
-
50
Y

i DTXSID3C Alternariol nr
C15H1205
272.256
-
-
-
39
Y

; DTXSID3GTenuazonic
C10H15NOC
197.234
Y
-
-
-
-


-------
Enhanced Data Sheets
MetFrag Input File (Beta) o
ToxPrint single fingerprints ©
Abstract Sifter Input File (Beta) ©
Synonyms and Identifiers e
* Related Substance relationships o
INPUT
DTXSID HAS RELATIONSHIP WITH
RELATED DTXSID
RELATED PREFERRED NAME
RELATED CASRN
emodin
DTXSI DSC Transformation Product
DTXSID60197420
omega-Hydroxyemodin
481-73-2

emodin
DTXSI DSC Transformation Product
DTXSID30191177
Questin
3774-64-9

emodin
DTXSI DSC Transformation Product
DTXSID80197684
Emodin anthrone
491-60-1

emodin
DTXSIDSCTransformation Product
DTXSID20200101
Physcione
521-61-9

emodin
DTXSI DSC Transformation Product
DTXSID70207049
2-Hydroxychrysophanol
58322-78-4

emodin
DTXSIDSCTransformation Product
DTXSID20211510
Aloe emodin anthrone
6247-99-0


-------
MASS AND
FORMULA
SEARCHING

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285.1364
Da
+
5
Da
ppm
Search Q
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(j) MS Ready Formula 0 O Exact Formula
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Searched by Mass: 255.7 364 +/- S.Q ppnn.
o
J
Pipeline
DTXSID: DTXSID3021 BO 5
CASRN: 94 62 2
TOXCAST: 59/374
Mass O'rfft ftfl0Q0S3
Ethartone, 1 iA -acetyl 1 -14 methcuc/phe_
DTX5IO: DTX SI DO0149360
CASRN: 112086-82-5
TOXCAST: -
Mass Diff. 0.000093
CjUJH X I TCHUM X
Hydrcmor phone
DTXSID DTXSlDa023133
CASRN: 466-99-9
TOXCAST:
MassDp 0.000093	
Kfofptenan 3.6 dio^ 7,6 dkiehydro-41,5 ¦
DTXSIDt DTXSiD401673C8
CASRN 16206 77 2
TOXCAST:
Mass Drff: D.000093
Morphine
OTXSID: DTXSID9023336
CASRN 57-27-2
TOXCAST:
Mass Orff OjO0OO9_3	
Q
O
^aTvrcdirw, {+/•
OTXSID QTXSID6016&190
CASRN 1668 06 6
TOXCAST:
Mass Diff: 0.000093

V.
"V
0—cw»

Ml

Norcodeinc
DTXSID: DTXSJD0O46327
CASRN: 467-15-2
TOXCAST: 0/79
Mass Diff: 0.000093
Carbamic acid, IphenylrnBthaxyltF^Bnyt..
DTXSID: DTXSI050171931
CASRN: 1B67-23-S
TOXCAST:
Mass Diff: 0.000093
Methanocie, (¦*-amino-2,5 didhanyphem...
DTXSlD: DTXS03Q71696
CASRN: 68568 55 fl
TOXCAST:
Mas Diff: 0000093
xo
'tx
7 Ssoqukiolinal 1,2,3,4-lrtrahydro-1 -[(4 -
DTXSID- DTXSID70176367
CASRN 2196 60-3
TOXCAST:
Masi Diff. 0.000093
65

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Step Five: Choose Data Fields to Download
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ppm
Enter Identifiers to Search (searches shoulc oe Iiinited to <5000 centif e-s
41.0265
56.02621
53.0265
58.041 s|
93.057S
113.9639
151.8754
69.9377
77.9872
I
LJ MS-Ready Formula(e) search is based on what we refer to as "Mass Spec (MS) Ready" structures. All chemicals
1 Exact Fo'mu a(e) Q within the database are treated in a manner such that all are desalted, mixtures are separated,
,	and stereochemistry is removed as Mass Spectrometry detects the major components of a salt
la Monoisotopic Mass ft	3	t-	j<	j	r
l^Jor mixture and is insensitive to stereochemistry. As an example, a search for the monoisotopic
<9? Display All Chemjmass of phenol will return phenol, sodium phenolate and calcium phenoxide. See the
publication for more details: https://doi.org/10.1186/s13321-018-0299-2.
66

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WORK IN
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CFM-ID >
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structures, to be accessible via Dashboard
DTXCID00916157
100	
90-
80-
£, 70-
I 60-
e
S 50"
! 40-
fVj
30-
20-
20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270

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Agency
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321.136493473
Da
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Mass or Formula must be entered before searching spectrum
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304.1332052 11.91SS475
1BS.0913404 7.30643.3686
123.044055B 0.53E34S262
196.0756654 5.206463115
216.1019051 4.7M46167S
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304.1332052 11,31
188.0913404 7.30!
123.0440569 6.53!
19S.O7588O4S.20!
216.1019051 470!
Peak Match
Search
TSV CSV
Chemical Structure ID
DTXCID1D1D4S191
DTXCID101181567
DTXCID50879086
DTXCIDGOS88349
DIXCID00B309DD
DTXGID10971178
DTXCID&D301242
DTXCID4070304S
DTXCID60349&S2
DTXCID1O310S4O
Showing 1 to 10 of 32 errtres
Chemical Structure ID
DTXCID10971176
DTXCID60301242
DTXCID40703048
DTXCI D60349982
DTXCID10316649
Score (10eV)
DTXCID101048191
0.22
DTXCID101181567
0.19
DTXCID50879086
0.17
DTX CI D60686349
0.14
DTXCID00830900
0 13
0.12
0.12
0.11
0.11
0.09
of Scores
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[2
3
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Spectral Viewer Comparison
DTXCFD50&79O86 ESI+
300-
»-
m-
70-
r«,
u
i *
¦»
30-
10-
0-
Input IfleV 20t*V 4(1CV
I'
|0.45
|().I6 |UD!I9
2
(.¦>.45
(ii. 16 [|n.m9{
|3
(0.45
|0.I6 [|0J029[
71

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Prototype Development
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Ewwonmont*! Protection
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AADashboard
atrazine
DB0a
° 1100% t| |A X A 3 V O ff %
o o o
o,
[ ]
n
K^-N
OOOADOO
Select properties to predict
T.E.S.T. E3 OPERA Search
® Exact
® Substructure
Search result	Show QJ Isotopically Labeled ~ Charged LI Salts or Mixtures Sort Similarity ~ —
N^\
<' N
N
nh2
N^N	N^N X	Nr<
[)	XN U ^ N	HzN—<• , N
nh2
N^N
H2N"N' H3C"n' u -X	h.c-^'n'-ch,
1	0.62	0.57 N "^§7
nh2
0.57
CI
.A.
N~N
Br
N ' N
Jo 'J l; {
CI N H)C N CH]
0.53	0.53	0.53

N	m ,i	N' N H3C^.X\V h3c^.A- !A	n-n	n'n	.
Br N Br	K N Tj"« "V-n-V ""V-V H3C0"V
5.5
CI N CI	Br N Br
0.5	0.5	0.5
N~N	j.
N - N
H3C^AVanh2
0.44	0.44	0.44
0.42
OH
N-^
HO-<' N
N^<
%
N - N
HjC-n-V
CHj
0.42
F
N^N
fA'n^5
N - N
ci ^ n''1' CI
N ' N	N^N
N ' N
f r I013 N^N
h^'n^ch, c|^"N'j *Th,™ "H*
HC ' * OH
0.42	0.42
0.4
0.4
0.4
N- H

«T°H
N^N
H3S*

HK%.
t-s0* sw V"!r	"x-'c ^vIC
KHl	-XHl
hbC.s
0.4	0.4
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0.4
J21
>rN H
N '>-H
FN CI
Ch« n.
HjC>l X'h ^ NH?
CHa
T
N - N
'«4
N - N-\, N ' N

C-m-N
L\, Jc
. •>
n"~n
0.38
Search result
Show y isotopically Labelec
HjC
N N hN	N N
LI f '** M *w	'FNhb	I. lV
K	>"N	H2N N CI uc^m^wj
h2n	hs n nh2
0.38	0.38	0.38	0.38
Nhfe
N^N
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0.38
72

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Prototype Development
A EPA
Unitad S:ales
Ewwonmont*! Protection
*a«ocY
DB0a
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Search result
HC^iC CH3
Show ~ Isotopically Labeled ~ C
CH3 CHs
Select properties to predict
T.E.S.T. |g OPERA Search
° Exact
° Substructure
° Similarity
® Molecular Formula
° Molecular Weight
Input formula (e.g. C6 H6):
C15H1602
50 i

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https7^^T^tQx.epa.gov/dashboard/DTXSID7020182
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Agilent Dataset
A EPA
Unitad S:ales
Ewwonmont*! Protection
*a«ocY
Agilent: "Mycotoxins and Metabolites
Personal Compound Database and Library"
Registered for next release...
Food
Mycotoxins PCDL
Perform truly comprehensive mycotoxin screening applications with the Mycotoxins and Related
Metabolites Personal Compound Database and Library (PCDL) for TOF and Q-TOF LC/MS systems.
Detailed acquisition method setup information allows fast ramp-up to full productivity.
REQUEST QUOTE
RELATED PRODUCTS
J_ - • ^
MassHunter PCDL Manager Compound view of
Mycotoxins PCDL
74

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Please help
v>EPA
Unitad S'Blos
Ewwonmont*! Protection
*a«ocY
Help grow the lists of Mycotoxins and Algal
Toxins - please suggest additions
Next up - structures of microviridins...
Email me at williams.antonv@epa.gov
75

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Conclusion
A EPA
Unitad S:ales
Ewwonmont*! Protection
*a«ocY
Building an integrated hub for environmental chemistry
Transparent access to data and models
Data QUALITY is a key focus - ongoing curation
Microcystins and algal toxins are two growing "lists"

m
EPA's CornpTox
			 Chemistry Dashboard ^
List...n lp^cr usts (User Interactions)
Aggregated Public Data

r
<&
5 Consumer Products & Categories,
Functional Use Data
1 Summarized In Vivo Data
tnVitroDB in Vitro Assay Data (ToxCast, 70*21,/
List 1	ChemProp Experimental &
Predicted Property Data
Models
Documentation for
Predictive Models
76

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Acknowledgements
A EPA
United Stales
Erwf#onmont»l Protection
Ao**ky
EPA-RTP
An enormous	team
from NCCT,	especially
software	development
Our curation	team
and focus on data
Multiple	centers	a
across the EPA
Many public domain
and open data contributors

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Antony Williams
NCCT, US EPA Office of Research and Development,
Williams.Antonv@epa.gov
ORCID: https://orcid.org/0000-0002-2668-4821
i
O Journal of Cheminformatics
DATA BASE	Open Access
The CompTox Chemistry Dashboard: a *
community data resource for environmental
chemistry
Antony J. Williams1* , Christopher M. Grulke1, Jeff Edwards' , Andrew D. McEachran2, Kamel Mansouri1,2,4,
Nancy C. Baker3, Grace Patlewicz1, Imran Shah1 John F.Wambaugh1, Richard S. Judson' and Ann M. Richard'
https://doi.orq/10.1186/s13321 -017-0247-6
78

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