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Showing metabocard for 5-Hydroxypyrazine-2-carboxylic acid (HMDB0246812)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:49:31 UTC
Update Date2021-09-26 22:56:07 UTC
HMDB IDHMDB0246812
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Hydroxypyrazine-2-carboxylic acid
Description5-Hydroxypyrazine-2-carboxylic acid belongs to the class of organic compounds known as pyrazine carboxylic acids. These are heterocyclic compounds containing a pyrazine ring substituted by one or more carboxylic acid groups. Based on a literature review a significant number of articles have been published on 5-Hydroxypyrazine-2-carboxylic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-hydroxypyrazine-2-carboxylic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Hydroxypyrazine-2-carboxylic acid 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 HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)


  Mrv1652309112101492D          

 10 10  0  0  0  0            999 V2000
    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 N   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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

HMDB0246812
     RDKit          3D
5-Hydroxypyrazine-2-carboxylic acid
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.6603   -1.3564   -1.0116 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0609   -0.3096   -0.6745 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7808    0.8730   -0.6775 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6575   -0.2818   -0.2843 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0100    0.8776    0.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2883    0.8792    0.4416 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0207   -0.2491    0.4570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2395   -0.2319    0.7947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -1.4137    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0784   -1.4146   -0.2687 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0189    1.3940    0.1438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5763    1.8008    0.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7899    1.7540    0.7235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9688   -2.3215    0.1014 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  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  9 14  1  0
M  END
Download

3D SDF for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)


  Mrv1652309112101492D          

 10 10  0  0  0  0            999 V2000
    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 N   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
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.6500    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246812

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CNC(=O)C=N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N2O3/c8-4-2-6-3(1-7-4)5(9)10/h1-2H,(H,7,8)(H,9,10)

> <INCHI_KEY>
CGQFCIHUUCMACC-UHFFFAOYSA-N

> <FORMULA>
C5H4N2O3

> <MOLECULAR_WEIGHT>
140.098

> <EXACT_MASS>
140.022191997

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.628981935182281

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-oxo-4,5-dihydropyrazine-2-carboxylic acid

> <ALOGPS_LOGP>
-1.11

> <JCHEM_LOGP>
-0.6662376249999998

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.642652502033995

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.6991712922907682

> <JCHEM_PKA_STRONGEST_BASIC>
-6.041489257662377

> <JCHEM_POLAR_SURFACE_AREA>
78.76

> <JCHEM_REFRACTIVITY>
31.886600000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-oxo-4H-pyrazine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

HMDB0246812
     RDKit          3D
5-Hydroxypyrazine-2-carboxylic acid
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.6603   -1.3564   -1.0116 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0609   -0.3096   -0.6745 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7808    0.8730   -0.6775 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6575   -0.2818   -0.2843 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0100    0.8776    0.0846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2883    0.8792    0.4416 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0207   -0.2491    0.4570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2395   -0.2319    0.7947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3791   -1.4137    0.0889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0784   -1.4146   -0.2687 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0189    1.3940    0.1438 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5763    1.8008    0.0810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7899    1.7540    0.7235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9688   -2.3215    0.1014 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  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  9 14  1  0
M  END
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PDB for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

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       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.000   0.000   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -0.000  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2    7                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    1                                                       
CONECT    8    2    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

COMPND    HMDB0246812
HETATM    1  O1  UNL     1       2.660  -1.356  -1.012  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.061  -0.310  -0.674  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.781   0.873  -0.678  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.657  -0.282  -0.284  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.010   0.878   0.085  1.00  0.00           C  
HETATM    6  N1  UNL     1      -1.288   0.879   0.442  1.00  0.00           N  
HETATM    7  C4  UNL     1      -2.021  -0.249   0.457  1.00  0.00           C  
HETATM    8  O3  UNL     1      -3.240  -0.232   0.795  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.379  -1.414   0.089  1.00  0.00           C  
HETATM   10  N2  UNL     1      -0.078  -1.415  -0.269  1.00  0.00           N  
HETATM   11  H1  UNL     1       3.019   1.394   0.144  1.00  0.00           H  
HETATM   12  H2  UNL     1       0.576   1.801   0.081  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.790   1.754   0.724  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.969  -2.322   0.101  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5    5   10
CONECT    5    6   12
CONECT    6    7   13
CONECT    7    8    8    9
CONECT    9   10   10   14
END
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SMILES for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

OC(=O)C1=CNC(=O)C=N1
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INCHI for HMDB0246812 (5-Hydroxypyrazine-2-carboxylic acid)

InChI=1S/C5H4N2O3/c8-4-2-6-3(1-7-4)5(9)10/h1-2H,(H,7,8)(H,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Hydroxypyrazine-2-carboxylateGenerator
5-Hydroxypyrazinoic acidHMDB
Chemical FormulaC5H4N2O3
Average Molecular Weight140.098
Monoisotopic Molecular Weight140.022191997
IUPAC Name5-oxo-4,5-dihydropyrazine-2-carboxylic acid
Traditional Name5-oxo-4H-pyrazine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=CNC(=O)C=N1
InChI Identifier
InChI=1S/C5H4N2O3/c8-4-2-6-3(1-7-4)5(9)10/h1-2H,(H,7,8)(H,9,10)
InChI KeyCGQFCIHUUCMACC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrazine carboxylic acids. These are heterocyclic compounds containing a pyrazine ring substituted by one or more carboxylic acid groups.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrazines
Direct ParentPyrazine carboxylic acids
Alternative Parents
Substituents
  • Pyrazine carboxylic acid
  • Vinylogous amide
  • Heteroaromatic compound
  • Lactam
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • 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
logP-1.1ALOGPS
logP-0.67ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)2.7ChemAxon
pKa (Strongest Basic)-6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area78.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity31.89 m³·mol⁻¹ChemAxon
Polarizability11.63 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]+125.75530932474
DeepCCS[M-H]-121.92630932474
DeepCCS[M-2H]-159.34930932474
DeepCCS[M+Na]+134.85730932474
AllCCS[M+H]+132.532859911
AllCCS[M+H-H2O]+128.132859911
AllCCS[M+NH4]+136.732859911
AllCCS[M+Na]+137.932859911
AllCCS[M-H]-124.832859911
AllCCS[M+Na-2H]-126.532859911
AllCCS[M+HCOO]-128.632859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.3585 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.86 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid626.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid353.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid66.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid233.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid66.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid275.2 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 Acid317.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)372.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid611.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid103.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid921.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid209.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid279.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate732.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA276.2 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water329.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Hydroxypyrazine-2-carboxylic acidOC(=O)C1=CNC(=O)C=N12152.9Standard polar33892256
5-Hydroxypyrazine-2-carboxylic acidOC(=O)C1=CNC(=O)C=N11405.4Standard non polar33892256
5-Hydroxypyrazine-2-carboxylic acidOC(=O)C1=CNC(=O)C=N11742.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Hydroxypyrazine-2-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C(=O)C=N11730.7Semi standard non polar33892256
5-Hydroxypyrazine-2-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C(=O)C=N11746.1Standard non polar33892256
5-Hydroxypyrazine-2-carboxylic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C)C(=O)C=N12072.4Standard polar33892256
5-Hydroxypyrazine-2-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C(=O)C=N12149.3Semi standard non polar33892256
5-Hydroxypyrazine-2-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C(=O)C=N12162.0Standard non polar33892256
5-Hydroxypyrazine-2-carboxylic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=CN([Si](C)(C)C(C)(C)C)C(=O)C=N12265.4Standard 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 ID142126
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound161825
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 ]