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Showing metabocard for 5-Nitrothiazole (HMDB0246829)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:50:33 UTC
Update Date2021-09-26 22:56:09 UTC
HMDB IDHMDB0246829
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Nitrothiazole
Description5-Nitrothiazole belongs to the class of organic compounds known as nitrothiazoles. Nitrothiazoles are compounds containing a thiazole ring which bears a nitro group. Based on a literature review a significant number of articles have been published on 5-Nitrothiazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-nitrothiazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Nitrothiazole 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 HMDB0246829 (5-Nitrothiazole)


  Mrv1652309112101502D          

  8  8  0  0  0  0            999 V2000
   -0.0997    0.6294    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 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  5  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  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  CHG  2   6   1   8  -1
M  END
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3D MOL for HMDB0246829 (5-Nitrothiazole)

HMDB0246829
     RDKit          3D
5-Nitrothiazole
 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.6301    0.6872    0.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9254   -0.2646   -0.1120 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5021   -1.4150   -0.5632 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4900   -0.1689   -0.0681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2729    0.8912    0.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5617    0.7583    0.3028 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0883   -0.3749   -0.1366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063   -1.3078   -0.5067 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2438    1.8092    0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1623   -0.6146   -0.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  4  1  0
  5  9  1  0
  7 10  1  0
M  CHG  2   2   1   3  -1
M  END
Download

3D SDF for HMDB0246829 (5-Nitrothiazole)


  Mrv1652309112101502D          

  8  8  0  0  0  0            999 V2000
   -0.0997    0.6294    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 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   0  5  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  2  0  0  0  0
  1  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
M  CHG  2   6   1   8  -1
M  END
> <DATABASE_ID>
HMDB0246829

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-][N+](=O)C1=CN=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C3H2N2O2S/c6-5(7)3-1-4-2-8-3/h1-2H

> <INCHI_KEY>
VVVCJCRUFSIVHI-UHFFFAOYSA-N

> <FORMULA>
C3H2N2O2S

> <MOLECULAR_WEIGHT>
130.12

> <EXACT_MASS>
129.983698486

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
10.266544992022041

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-nitro-1,3-thiazole

> <ALOGPS_LOGP>
0.90

> <JCHEM_LOGP>
0.7380187573333334

> <ALOGPS_LOGS>
-1.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.0283308736141112

> <JCHEM_POLAR_SURFACE_AREA>
56.03

> <JCHEM_REFRACTIVITY>
26.746800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-nitro-1,3-thiazole

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0246829 (5-Nitrothiazole)

HMDB0246829
     RDKit          3D
5-Nitrothiazole
 10 10  0  0  0  0  0  0  0  0999 V2000
   -2.6301    0.6872    0.2559 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9254   -0.2646   -0.1120 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.5021   -1.4150   -0.5632 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.4900   -0.1689   -0.0681 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2729    0.8912    0.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5617    0.7583    0.3028 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0883   -0.3749   -0.1366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063   -1.3078   -0.5067 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2438    1.8092    0.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1623   -0.6146   -0.2251 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  4  1  0
  5  9  1  0
  7 10  1  0
M  CHG  2   2   1   3  -1
M  END
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PDB for HMDB0246829 (5-Nitrothiazole)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0       2.306   1.175   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+1
HETATM    7  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O-1
CONECT    1    2    5                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    2    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0246829 (5-Nitrothiazole)

COMPND    HMDB0246829
HETATM    1  O1  UNL     1      -2.630   0.687   0.256  1.00  0.00           O  
HETATM    2  N1  UNL     1      -1.925  -0.265  -0.112  1.00  0.00           N1+
HETATM    3  O2  UNL     1      -2.502  -1.415  -0.563  1.00  0.00           O1-
HETATM    4  C1  UNL     1      -0.490  -0.169  -0.068  1.00  0.00           C  
HETATM    5  C2  UNL     1       0.273   0.891   0.349  1.00  0.00           C  
HETATM    6  N2  UNL     1       1.562   0.758   0.303  1.00  0.00           N  
HETATM    7  C3  UNL     1       2.088  -0.375  -0.137  1.00  0.00           C  
HETATM    8  S1  UNL     1       0.706  -1.308  -0.507  1.00  0.00           S  
HETATM    9  H1  UNL     1      -0.244   1.809   0.704  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.162  -0.615  -0.225  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5    8
CONECT    5    6    9
CONECT    6    7    7
CONECT    7    8   10
END
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SMILES for HMDB0246829 (5-Nitrothiazole)

[O-][N+](=O)C1=CN=CS1
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INCHI for HMDB0246829 (5-Nitrothiazole)

InChI=1S/C3H2N2O2S/c6-5(7)3-1-4-2-8-3/h1-2H
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC3H2N2O2S
Average Molecular Weight130.12
Monoisotopic Molecular Weight129.983698486
IUPAC Name5-nitro-1,3-thiazole
Traditional Name5-nitro-1,3-thiazole
CAS Registry NumberNot Available
SMILES
[O-][N+](=O)C1=CN=CS1
InChI Identifier
InChI=1S/C3H2N2O2S/c6-5(7)3-1-4-2-8-3/h1-2H
InChI KeyVVVCJCRUFSIVHI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitrothiazoles. Nitrothiazoles are compounds containing a thiazole ring which bears a nitro group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassAzoles
Sub ClassThiazoles
Direct ParentNitrothiazoles
Alternative Parents
Substituents
  • Nitroaromatic compound
  • Nitrothiazole
  • Heteroaromatic compound
  • C-nitro compound
  • Organic nitro compound
  • Organic oxoazanium
  • Allyl-type 1,3-dipolar organic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Azacycle
  • Organic 1,3-dipolar compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic zwitterion
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP0.9ALOGPS
logP0.74ChemAxon
logS-1.8ALOGPS
pKa (Strongest Basic)-2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area56.03 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity26.75 m³·mol⁻¹ChemAxon
Polarizability10.27 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+116.4430932474
DeepCCS[M-H]-114.09630932474
DeepCCS[M-2H]-149.81130932474
DeepCCS[M+Na]+124.1830932474
AllCCS[M+H]+126.232859911
AllCCS[M+H-H2O]+121.632859911
AllCCS[M+NH4]+130.632859911
AllCCS[M+Na]+131.832859911
AllCCS[M-H]-119.832859911
AllCCS[M+Na-2H]-122.332859911
AllCCS[M+HCOO]-125.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.1983 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.33 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid885.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid406.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid115.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid294.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid80.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid303.1 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 Acid412.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)745.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid708.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid81.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1049.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid251.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid353.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate772.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA334.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water286.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Nitrothiazole[O-][N+](=O)C1=CN=CS12014.3Standard polar33892256
5-Nitrothiazole[O-][N+](=O)C1=CN=CS11271.9Standard non polar33892256
5-Nitrothiazole[O-][N+](=O)C1=CN=CS11178.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Nitrothiazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-004l-9800000000-06156637205ccef2cf2e2021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Nitrothiazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 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 NMR1H NMR Spectrum (1D, 1000 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, 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 NMR1H NMR Spectrum (1D, 600 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, 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 NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H 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 ID471687
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound541661
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 ]