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Showing metabocard for Epigoitrin (HMDB0251849)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 09:29:09 UTC
Update Date2021-09-26 23:04:07 UTC
HMDB IDHMDB0251849
Secondary Accession NumbersNone
Metabolite Identification
Common NameEpigoitrin
Description5-ethenyl-4,5-dihydro-1,3-oxazole-2-thiol belongs to the class of organic compounds known as oxazolidines. Oxazolidines are compounds containing an oxazolidine moiety, which consists of a saturated aliphatic five-member ring with one oxygen atom, one nitrogen, three carbon atoms, and two double bonds. Based on a literature review very few articles have been published on 5-ethenyl-4,5-dihydro-1,3-oxazole-2-thiol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Epigoitrin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Epigoitrin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0251849 (Epigoitrin)


  Mrv1533004161521062D          

  8  8  0  0  0  0            999 V2000
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
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3D MOL for HMDB0251849 (Epigoitrin)

HMDB0251849
     RDKit          3D
Epigoitrin
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.3252    0.0168   -0.4362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326   -0.9272   -0.2424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0414   -0.6220    0.0646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2745    0.8352    0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7212    0.8223    0.0959 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0465   -0.3284   -0.6698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5539   -0.7734   -1.1418 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8658   -1.0380   -0.9661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3695   -0.1685   -0.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0521    1.0792   -0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7476   -1.9589   -0.3145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3056   -1.1293    0.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0705    1.3847   -0.7481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1004    1.3014    1.0964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3718    1.5062    0.5147 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
M  END
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3D SDF for HMDB0251849 (Epigoitrin)


  Mrv1533004161521062D          

  8  8  0  0  0  0            999 V2000
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251849

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CC1CNC(=S)O1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NOS/c1-2-4-3-6-5(8)7-4/h2,4H,1,3H2,(H,6,8)

> <INCHI_KEY>
UZQVYLOFLQICCT-UHFFFAOYSA-N

> <FORMULA>
C5H7NOS

> <MOLECULAR_WEIGHT>
129.18

> <EXACT_MASS>
129.024835023

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
13.207490216103324

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-ethenyl-1,3-oxazolidine-2-thione

> <ALOGPS_LOGP>
-0.02

> <JCHEM_LOGP>
1.3220404079999997

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.641236134134513

> <JCHEM_POLAR_SURFACE_AREA>
21.259999999999998

> <JCHEM_REFRACTIVITY>
35.841

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.03e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
goitrin

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0251849 (Epigoitrin)

HMDB0251849
     RDKit          3D
Epigoitrin
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.3252    0.0168   -0.4362 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326   -0.9272   -0.2424 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0414   -0.6220    0.0646 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2745    0.8352    0.1667 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7212    0.8223    0.0959 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0465   -0.3284   -0.6698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5539   -0.7734   -1.1418 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8658   -1.0380   -0.9661 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3695   -0.1685   -0.6665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0521    1.0792   -0.3731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7476   -1.9589   -0.3145 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3056   -1.1293    0.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0705    1.3847   -0.7481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1004    1.3014    1.0964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3718    1.5062    0.5147 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  3  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
M  END
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PDB for HMDB0251849 (Epigoitrin)

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.830  -0.290   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0      -0.615  -1.536   0.000  0.00  0.00           S+0
HETATM    8  O   UNK     0      -0.186   1.175   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    3                                                       
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0251849 (Epigoitrin)

COMPND    HMDB0251849
HETATM    1  C1  UNL     1      -2.325   0.017  -0.436  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.433  -0.927  -0.242  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.041  -0.622   0.065  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.274   0.835   0.167  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.721   0.822   0.096  1.00  0.00           N  
HETATM    6  C5  UNL     1       2.046  -0.328  -0.670  1.00  0.00           C  
HETATM    7  S1  UNL     1       3.554  -0.773  -1.142  1.00  0.00           S  
HETATM    8  O1  UNL     1       0.866  -1.038  -0.966  1.00  0.00           O  
HETATM    9  H1  UNL     1      -3.369  -0.168  -0.666  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.052   1.079  -0.373  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.748  -1.959  -0.315  1.00  0.00           H  
HETATM   12  H4  UNL     1       0.306  -1.129   0.983  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.070   1.385  -0.748  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.100   1.301   1.096  1.00  0.00           H  
HETATM   15  H7  UNL     1       2.372   1.506   0.515  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    8   12
CONECT    4    5   13   14
CONECT    5    6   15
CONECT    6    7    7    8
END
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SMILES for HMDB0251849 (Epigoitrin)

C=CC1CNC(=S)O1
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INCHI for HMDB0251849 (Epigoitrin)

InChI=1S/C5H7NOS/c1-2-4-3-6-5(8)7-4/h2,4H,1,3H2,(H,6,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Vinyloxazolidine-2-thioneMeSH
GoitrinMeSH
5-Vinyl-2-thiooxazolidoneMeSH
5-Vinyloxazolidin-2-thioneMeSH
EpigoitrinMeSH
Goitrin, (R)-isomerMeSH
Goitrin, (+-)-isomerMeSH
Goitrin, (S)-isomerMeSH
Chemical FormulaC5H7NOS
Average Molecular Weight129.18
Monoisotopic Molecular Weight129.024835023
IUPAC Name5-ethenyl-1,3-oxazolidine-2-thione
Traditional Namegoitrin
CAS Registry NumberNot Available
SMILES
C=CC1CNC(=S)O1
InChI Identifier
InChI=1S/C5H7NOS/c1-2-4-3-6-5(8)7-4/h2,4H,1,3H2,(H,6,8)
InChI KeyUZQVYLOFLQICCT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as oxazolidines. Oxazolidines are compounds containing an oxazolidine moiety, which consists of a saturated aliphatic five-member ring with one oxygen atom, one nitrogen, three carbon atoms, and two double bonds.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzolidines
Sub ClassOxazolidines
Direct ParentOxazolidines
Alternative Parents
Substituents
  • Thiocarbamic acid ester
  • Oxazolidine
  • Thiocarbamic acid derivative
  • Oxacycle
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.02ALOGPS
logP1.32ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)8.64ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area21.26 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.84 m³·mol⁻¹ChemAxon
Polarizability13.21 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+129.43830932474
DeepCCS[M-H]-127.4530932474
DeepCCS[M-2H]-163.15730932474
DeepCCS[M+Na]+137.79230932474
AllCCS[M+H]+126.332859911
AllCCS[M+H-H2O]+121.632859911
AllCCS[M+NH4]+130.832859911
AllCCS[M+Na]+132.032859911
AllCCS[M-H]-124.032859911
AllCCS[M+Na-2H]-126.632859911
AllCCS[M+HCOO]-129.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
EpigoitrinC=CC1CNC(=S)O12290.3Standard polar33892256
EpigoitrinC=CC1CNC(=S)O11237.2Standard non polar33892256
EpigoitrinC=CC1CNC(=S)O11539.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Epigoitrin,1TMS,isomer #1C=CC1CN([Si](C)(C)C)C(=S)O11341.4Semi standard non polar33892256
Epigoitrin,1TMS,isomer #1C=CC1CN([Si](C)(C)C)C(=S)O11361.4Standard non polar33892256
Epigoitrin,1TMS,isomer #1C=CC1CN([Si](C)(C)C)C(=S)O11896.6Standard polar33892256
Epigoitrin,1TBDMS,isomer #1C=CC1CN([Si](C)(C)C(C)(C)C)C(=S)O11556.6Semi standard non polar33892256
Epigoitrin,1TBDMS,isomer #1C=CC1CN([Si](C)(C)C(C)(C)C)C(=S)O11595.1Standard non polar33892256
Epigoitrin,1TBDMS,isomer #1C=CC1CN([Si](C)(C)C(C)(C)C)C(=S)O12044.7Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Epigoitrin GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9000000000-df1d69d1d915bd6417562021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Epigoitrin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 10V, Positive-QTOFsplash10-001i-1900000000-ac274fa50ceb0d05a5d82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 20V, Positive-QTOFsplash10-0f89-8900000000-b063084e2fe0b29c05a42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 40V, Positive-QTOFsplash10-0zfu-9000000000-b00550ce8b805f3bae8a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 10V, Negative-QTOFsplash10-01tc-9400000000-0efa33318f266b8b0c362021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 20V, Negative-QTOFsplash10-06w9-9100000000-e58972803d4177b7e9c72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Epigoitrin 40V, Negative-QTOFsplash10-0a4i-9000000000-3cea8b89ef6cd0ce9f982021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2299106
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound102419
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]