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Showing metabocard for Isothiocyanatobenzene (HMDB0253699)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:30:51 UTC
Update Date2021-09-26 23:07:06 UTC
HMDB IDHMDB0253699
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsothiocyanatobenzene
DescriptionPhenyl isothiocyanate, also known as benzene-1-isothiocyanate or phenyl mustard oil, belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene. Phenyl isothiocyanate is a chemical compound of cyanide. Exposure to high levels of cyanide for a short time harms the brain and heart and can even cause coma, seizures, apnea, cardiac arrest and death. Phenyl isothiocyanate is an extremely weak basic (essentially neutral) compound (based on its pKa). Phenyl isothiocyanate is a potentially toxic compound. The binding of cyanide to this cytochrome prevents transport of electrons from cytochrome c oxidase to oxygen. Cyanide binds to the ferric ion of methemoglobin to form inactive cyanmethemoglobin. SKIN: should be treated immediately by rinsing the affected parts in cold running water for at least 15 minutes, followed by thorough washing with soap and water. INHALATION: supply fresh air. This compound has been identified in human blood as reported by (PMID: 31557052 ). Isothiocyanatobenzene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Isothiocyanatobenzene 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 HMDB0253699 (Isothiocyanatobenzene)


  Mrv0541 02241204582D          

  9  9  0  0  0  0            999 V2000
   -0.7145    2.8875    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
M  END
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3D MOL for HMDB0253699 (Isothiocyanatobenzene)

HMDB0253699
     RDKit          3D
Isothiocyanatobenzene
 14 14  0  0  0  0  0  0  0  0999 V2000
    4.1747    0.1858    0.5584 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9453    0.0224   -0.4675 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8931   -0.0767   -1.1660 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6196   -0.0461   -0.5727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0186    1.1593   -0.4006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2756    1.1982    0.1842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8777    0.0362    0.5884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2441   -1.1978    0.4215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0289   -1.2202   -0.1725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4876    2.0523   -0.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7459    2.1548    0.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8558    0.0102    1.0493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6959   -2.1280    0.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5645   -2.1504   -0.3255 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
  9 14  1  0
M  END
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3D SDF for HMDB0253699 (Isothiocyanatobenzene)


  Mrv0541 02241204582D          

  9  9  0  0  0  0            999 V2000
   -0.7145    2.8875    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  4  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253699

> <DATABASE_NAME>
hmdb

> <SMILES>
S=C=NC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H5NS/c9-6-8-7-4-2-1-3-5-7/h1-5H

> <INCHI_KEY>
QKFJKGMPGYROCL-UHFFFAOYSA-N

> <FORMULA>
C7H5NS

> <MOLECULAR_WEIGHT>
135.186

> <EXACT_MASS>
135.014269855

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
13.988573491648118

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
isothiocyanatobenzene

> <ALOGPS_LOGP>
3.08

> <JCHEM_LOGP>
2.9950710430000003

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.051819895086532286

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
43.120900000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phenylisothiocyanate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253699 (Isothiocyanatobenzene)

HMDB0253699
     RDKit          3D
Isothiocyanatobenzene
 14 14  0  0  0  0  0  0  0  0999 V2000
    4.1747    0.1858    0.5584 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.9453    0.0224   -0.4675 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8931   -0.0767   -1.1660 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6196   -0.0461   -0.5727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0186    1.1593   -0.4006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2756    1.1982    0.1842 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8777    0.0362    0.5884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2441   -1.1978    0.4215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0289   -1.2202   -0.1725 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4876    2.0523   -0.7316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7459    2.1548    0.3038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8558    0.0102    1.0493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6959   -2.1280    0.7309 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5645   -2.1504   -0.3255 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  5 10  1  0
  6 11  1  0
  7 12  1  0
  8 13  1  0
  9 14  1  0
M  END
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PDB for HMDB0253699 (Isothiocyanatobenzene)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  S   UNK     0      -1.334   5.390   0.000  0.00  0.00           S+0
HETATM    2  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0253699 (Isothiocyanatobenzene)

COMPND    HMDB0253699
HETATM    1  S1  UNL     1       4.175   0.186   0.558  1.00  0.00           S  
HETATM    2  C1  UNL     1       2.945   0.022  -0.468  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.893  -0.077  -1.166  1.00  0.00           N  
HETATM    4  C2  UNL     1       0.620  -0.046  -0.573  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.019   1.159  -0.401  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.276   1.198   0.184  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.878   0.036   0.588  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.244  -1.198   0.421  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.029  -1.220  -0.173  1.00  0.00           C  
HETATM   10  H1  UNL     1       0.488   2.052  -0.732  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.746   2.155   0.304  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.856   0.010   1.049  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.696  -2.128   0.731  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.565  -2.150  -0.326  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    3
CONECT    3    4
CONECT    4    5    5    9
CONECT    5    6   10
CONECT    6    7    7   11
CONECT    7    8   12
CONECT    8    9    9   13
CONECT    9   14
END
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SMILES for HMDB0253699 (Isothiocyanatobenzene)

S=C=NC1=CC=CC=C1
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INCHI for HMDB0253699 (Isothiocyanatobenzene)

InChI=1S/C7H5NS/c9-6-8-7-4-2-1-3-5-7/h1-5H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Benzene-1-isothiocyanateChEBI
Isothiocyanic acid phenyl esterChEBI
Phenyl mustard oilChEBI
PhenylsenfoelChEBI
PITCChEBI
Benzene-1-isothiocyanic acidGenerator
Isothiocyanate phenyl esterGenerator
Phenyl isothiocyanic acidGenerator
PhenylisothiocyanateMeSH
Chemical FormulaC7H5NS
Average Molecular Weight135.186
Monoisotopic Molecular Weight135.014269855
IUPAC Nameisothiocyanatobenzene
Traditional Namephenylisothiocyanate
CAS Registry NumberNot Available
SMILES
S=C=NC1=CC=CC=C1
InChI Identifier
InChI=1S/C7H5NS/c9-6-8-7-4-2-1-3-5-7/h1-5H
InChI KeyQKFJKGMPGYROCL-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassNot Available
Direct ParentBenzene and substituted derivatives
Alternative Parents
Substituents
  • Monocyclic benzene moiety
  • Isothiocyanate
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organonitrogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot 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
logP3.08ALOGPS
logP3ChemAxon
logS-3ALOGPS
pKa (Strongest Basic)0.052ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity43.12 m³·mol⁻¹ChemAxon
Polarizability13.99 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]+123.81230932474
DeepCCS[M-H]-120.85330932474
DeepCCS[M-2H]-157.56830932474
DeepCCS[M+Na]+132.66930932474
AllCCS[M+H]+129.732859911
AllCCS[M+H-H2O]+125.232859911
AllCCS[M+NH4]+133.932859911
AllCCS[M+Na]+135.132859911
AllCCS[M-H]-123.532859911
AllCCS[M+Na-2H]-125.732859911
AllCCS[M+HCOO]-128.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202213.1112 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.89 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2150.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid620.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid220.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid436.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid309.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid604.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid666.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)501.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1274.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid455.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1323.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid434.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid469.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate705.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA430.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water165.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IsothiocyanatobenzeneS=C=NC1=CC=CC=C12005.6Standard polar33892256
IsothiocyanatobenzeneS=C=NC1=CC=CC=C11180.6Standard non polar33892256
IsothiocyanatobenzeneS=C=NC1=CC=CC=C11206.6Semi standard non polar33892256
Spectra
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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPhenyl_isothiocyanate
METLIN IDNot Available
PubChem Compound7673
PDB IDNot Available
ChEBI ID85103
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 ]