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Showing metabocard for Pteridine (HMDB0256912)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 17:32:20 UTC
Update Date2021-10-01 23:01:59 UTC
HMDB IDHMDB0256912
Secondary Accession NumbersNone
Metabolite Identification
Common NamePteridine
Descriptionpteridine, also known as azinepurine, belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine. pteridine exists in all living organisms, ranging from bacteria to humans. Based on a literature review very few articles have been published on pteridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pteridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pteridine 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 HMDB0256912 (Pteridine)

Structure #1
  Mrv0541 02241206062D          

 10 11  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
   -1.4289    0.8250    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
    1.4289    0.8250    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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  2  0  0  0  0
  2  9  2  0  0  0  0
  3  5  2  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
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3D MOL for HMDB0256912 (Pteridine)

HMDB0256912
     RDKit          3D
Pteridine
 14 15  0  0  0  0  0  0  0  0999 V2000
    2.1034    0.9118    0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2513   -0.4370    0.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1999   -1.2762    0.2436 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0468   -0.7992    0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1333   -1.5876    0.1080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3851   -1.1233   -0.0411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5427    0.2017   -0.2132 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4752    1.0437   -0.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1907    0.5626   -0.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8589    1.4072   -0.1066 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9408    1.6079    0.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2522   -0.8295    0.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2421   -1.7904   -0.0240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5904    2.1084   -0.3733 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  1  1  0
  9  4  1  0
  1 11  1  0
  2 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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3D SDF for HMDB0256912 (Pteridine)

Structure #1
  Mrv0541 02241206062D          

 10 11  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
   -1.4289    0.8250    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
    1.4289    0.8250    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
    1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  2  0  0  0  0
  2  9  2  0  0  0  0
  3  5  2  0  0  0  0
  3  7  1  0  0  0  0
  4  7  2  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256912

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=NC2=CN=CN=C2N=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H4N4/c1-2-9-6-5(8-1)3-7-4-10-6/h1-4H

> <INCHI_KEY>
CPNGPNLZQNNVQM-UHFFFAOYSA-N

> <FORMULA>
C6H4N4

> <MOLECULAR_WEIGHT>
132.1228

> <EXACT_MASS>
132.043596148

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
11.997759104080695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pteridine

> <ALOGPS_LOGP>
-0.15

> <JCHEM_LOGP>
-0.2994274356666666

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.472379209304082

> <JCHEM_POLAR_SURFACE_AREA>
51.56

> <JCHEM_REFRACTIVITY>
35.6875

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.58e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pteridine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0256912 (Pteridine)

HMDB0256912
     RDKit          3D
Pteridine
 14 15  0  0  0  0  0  0  0  0999 V2000
    2.1034    0.9118    0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2513   -0.4370    0.2201 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1999   -1.2762    0.2436 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0468   -0.7992    0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1333   -1.5876    0.1080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3851   -1.1233   -0.0411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5427    0.2017   -0.2132 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4752    1.0437   -0.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1907    0.5626   -0.0823 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8589    1.4072   -0.1066 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9408    1.6079    0.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2522   -0.8295    0.3419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2421   -1.7904   -0.0240 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5904    2.1084   -0.3733 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  1  1  0
  9  4  1  0
  1 11  1  0
  2 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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PDB for HMDB0256912 (Pteridine)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
CONECT    1    2    8                                                       
CONECT    2    1    9                                                       
CONECT    3    5    7                                                       
CONECT    4    7   10                                                       
CONECT    5    3    6    8                                                  
CONECT    6    5    9   10                                                  
CONECT    7    3    4                                                       
CONECT    8    1    5                                                       
CONECT    9    2    6                                                       
CONECT   10    4    6                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0256912 (Pteridine)

COMPND    HMDB0256912
HETATM    1  C1  UNL     1       2.103   0.912   0.046  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.251  -0.437   0.220  1.00  0.00           C  
HETATM    3  N1  UNL     1       1.200  -1.276   0.244  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.047  -0.799   0.093  1.00  0.00           C  
HETATM    5  N2  UNL     1      -1.133  -1.588   0.108  1.00  0.00           N  
HETATM    6  C4  UNL     1      -2.385  -1.123  -0.041  1.00  0.00           C  
HETATM    7  N3  UNL     1      -2.543   0.202  -0.213  1.00  0.00           N  
HETATM    8  C5  UNL     1      -1.475   1.044  -0.236  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.191   0.563  -0.082  1.00  0.00           C  
HETATM   10  N4  UNL     1       0.859   1.407  -0.107  1.00  0.00           N  
HETATM   11  H1  UNL     1       2.941   1.608   0.024  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.252  -0.829   0.342  1.00  0.00           H  
HETATM   13  H3  UNL     1      -3.242  -1.790  -0.024  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.590   2.108  -0.373  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    4
CONECT    4    5    9
CONECT    5    6    6
CONECT    6    7   13
CONECT    7    8    8
CONECT    8    9   14
CONECT    9   10   10
END
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SMILES for HMDB0256912 (Pteridine)

C1=NC2=CN=CN=C2N=C1
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INCHI for HMDB0256912 (Pteridine)

InChI=1S/C6H4N4/c1-2-9-6-5(8-1)3-7-4-10-6/h1-4H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3,5,8-TetraazanaphthaleneChEBI
AzinepurineChEBI
Chemical FormulaC6H4N4
Average Molecular Weight132.1228
Monoisotopic Molecular Weight132.043596148
IUPAC Namepteridine
Traditional Namepteridine
CAS Registry NumberNot Available
SMILES
C1=NC2=CN=CN=C2N=C1
InChI Identifier
InChI=1S/C6H4N4/c1-2-9-6-5(8-1)3-7-4-10-6/h1-4H
InChI KeyCPNGPNLZQNNVQM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pteridines and derivatives. These are polycyclic aromatic compounds containing a pteridine moiety, which consists of a pyrimidine fused to a pyrazine ring to form pyrimido(4,5-b)pyrazine.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPteridines and derivatives
Sub ClassNot Available
Direct ParentPteridines and derivatives
Alternative Parents
Substituents
  • Pteridine
  • Pyrimidine
  • Pyrazine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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
logP-0.15ALOGPS
logP-0.3ChemAxon
logS-0.57ALOGPS
pKa (Strongest Basic)2.47ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area51.56 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity35.69 m³·mol⁻¹ChemAxon
Polarizability12 ųChemAxon
Number of Rings2ChemAxon
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]+125.1430932474
DeepCCS[M-H]-121.88530932474
DeepCCS[M-2H]-158.98530932474
DeepCCS[M+Na]+134.15930932474
AllCCS[M+H]+127.632859911
AllCCS[M+H-H2O]+122.732859911
AllCCS[M+NH4]+132.232859911
AllCCS[M+Na]+133.532859911
AllCCS[M-H]-123.332859911
AllCCS[M+Na-2H]-124.532859911
AllCCS[M+HCOO]-125.932859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.91 minutes32390414
Predicted by Siyang on May 30, 20228.9366 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.21 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1490.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid326.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid120.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid246.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid120.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid292.4 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 Acid374.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)103.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid626.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid75.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid801.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid202.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid252.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate331.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA220.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water119.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PteridineC1=NC2=CN=CN=C2N=C11853.7Standard polar33892256
PteridineC1=NC2=CN=CN=C2N=C11340.8Standard non polar33892256
PteridineC1=NC2=CN=CN=C2N=C11378.2Semi 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 IDC00007501
Chemspider ID1014
KEGG Compound IDC07581
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPteridine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27601
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 ]

Enzymes

Enzyme Details
1. E3 ubiquitin-protein ligase MYCBP2
General function:
Not Available
Specific function:
Atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues (By similarity). Shows esterification activity towards both threonine and serine, with a preference for threonine, and acts via two essential catalytic cysteine residues that relay ubiquitin to its substrate via thioester intermediates (By similarity). Interacts with the E2 enzymes UBE2D1, UBE2D3, UBE2E1 and UBE2L3 (By similarity). Plays a key role in neural development, probably by mediating ubiquitination of threonine residues on target proteins (By similarity). Involved in different processes such as regulation of neurite outgrowth, synaptic growth, synaptogenesis and axon degeneration (By similarity). Required in the visual system for correct fasciculation, targeting and mapping of retinal axons (PubMed:15590740). Acts as a regulator of pteridine synthesis (PubMed:15617681). May play a role in the regulation of the circadian clock gene expression (By similarity).
Gene Name:
MYCBP2
Uniprot ID:
F1RD40
Molecular weight:
501843.035