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Showing metabocard for Pyrimidine (HMDB0003361)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-12 19:21:07 UTC
Update Date2023-02-21 17:16:38 UTC
HMDB IDHMDB0003361
Secondary Accession Numbers
  • HMDB03361
Metabolite Identification
Common NamePyrimidine
DescriptionPyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring. Pyrimidines are heterocyclic, six-membered, nitrogen-containing carbon ring structures, with uracil, cytosine and thymine being the basal structures of ribose-containing nucleosides (uridine, cytidine and thymidine respectively), or deoxyribose-containing deoxynucleosides, and their corresponding ribonucleotides or deoxyribonucleotides. Pyrimidines serve essential functions in human metabolism as ribonucleotide bases in RNA (uracil and cytosine), and as deoxyribonucleotide bases in DNA (cytosine and thymine), and are linked by phosphodiester bridges to purine nucleotides in double-stranded DNA, in both the nucleus and the mitochondria. Pyrimidine activated sugars are also involved in polysaccharide and phospholipid synthesis, glucuronidation in detoxification processes, glycosylation of proteins and lipids and in the recently identified novel endothelium-derived vasoactive dinucleotides. Pyrimidines are synthesized de novo from simple precursors. Synthesis occurs in six steps, with cellular compartmentalization of specific steps in the cytosol or mitochondria, enabling changes in metabolic rate with need. Pyrimidine synthesis differs from purine synthesis, in that the single pyrimidine ring is assembled first and is then linked to ribose phosphate to form UMP. The enzymes that catalyse UMP synthesis, CAD [carbamoylphosphate synthetase II (CPSII), aspartate transcarbamoylase (ATCasea) and dihydroorotase (DHOase)], dihydroorotate dehydrogenase (DHODH) and uridine monophosphate synthase (UMPS), are encoded by only three genes - CAD, DHODH and UMPS (chromosomal locations 2p21, 16q22 and 3q13, respectively). (PMID:16098809 ).
Structure
Data?1676999798
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003361 (Pyrimidine)

  Mrv1652305271900272D          

  6  6  0  0  0  0            999 V2000
   26.3564  -10.7234    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   27.0708  -11.9609    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -10.7234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.0708  -10.3109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -11.5484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3564  -11.5484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  6  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
M  END
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3D MOL for HMDB0003361 (Pyrimidine)

HMDB0003361
     RDKit          3D
Pyrimidine
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.0896    0.3260    0.0497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -1.0060    0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5722   -1.3844   -0.0169 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5479   -0.4597   -0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2200    0.8452   -0.0649 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0712    1.2561   -0.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1286    0.6223    0.0973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5436   -1.7247    0.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5831   -0.7700   -0.1179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    2.2951   -0.0003 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  1  1  0
  1  7  1  0
  2  8  1  0
  4  9  1  0
  6 10  1  0
M  END
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3D SDF for HMDB0003361 (Pyrimidine)

  Mrv1652305271900272D          

  6  6  0  0  0  0            999 V2000
   26.3564  -10.7234    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   27.0708  -11.9609    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -10.7234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.0708  -10.3109    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.7854  -11.5484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3564  -11.5484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  2  0  0  0  0
  1  6  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003361

> <DATABASE_NAME>
hmdb

> <SMILES>
C1=CN=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H

> <INCHI_KEY>
CZPWVGJYEJSRLH-UHFFFAOYSA-N

> <FORMULA>
C4H4N2

> <MOLECULAR_WEIGHT>
80.088

> <EXACT_MASS>
80.037448138

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
7.618895366217213

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyrimidine

> <ALOGPS_LOGP>
-0.21

> <JCHEM_LOGP>
0.049735456000000094

> <ALOGPS_LOGS>
0.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
1.580976790148238

> <JCHEM_POLAR_SURFACE_AREA>
25.78

> <JCHEM_REFRACTIVITY>
22.722299999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.70e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrimidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0003361 (Pyrimidine)

HMDB0003361
     RDKit          3D
Pyrimidine
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.0896    0.3260    0.0497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -1.0060    0.0428 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5722   -1.3844   -0.0169 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5479   -0.4597   -0.0707 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2200    0.8452   -0.0649 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0712    1.2561   -0.0061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1286    0.6223    0.0973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5436   -1.7247    0.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5831   -0.7700   -0.1179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    2.2951   -0.0003 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  1  1  0
  1  7  1  0
  2  8  1  0
  4  9  1  0
  6 10  1  0
M  END
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PDB for HMDB0003361 (Pyrimidine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  N   UNK     0      49.199 -20.017   0.000  0.00  0.00           N+0
HETATM    2  N   UNK     0      50.532 -22.327   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      51.866 -20.017   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      50.532 -19.247   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      51.866 -21.557   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      49.199 -21.557   0.000  0.00  0.00           C+0
CONECT    1    4    6                                                       
CONECT    2    5    6                                                       
CONECT    3    4    5                                                       
CONECT    4    1    3                                                       
CONECT    5    2    3                                                       
CONECT    6    1    2                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0003361 (Pyrimidine)

COMPND    HMDB0003361
HETATM    1  C1  UNL     1      -1.090   0.326   0.050  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.733  -1.006   0.043  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.572  -1.384  -0.017  1.00  0.00           N  
HETATM    4  C3  UNL     1       1.548  -0.460  -0.071  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.220   0.845  -0.065  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.071   1.256  -0.006  1.00  0.00           C  
HETATM    7  H1  UNL     1      -2.129   0.622   0.097  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.544  -1.725   0.087  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.583  -0.770  -0.118  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.357   2.295  -0.000  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    4
CONECT    4    5    9
CONECT    5    6    6
CONECT    6   10
END
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SMILES for HMDB0003361 (Pyrimidine)

C1=CN=CN=C1
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INCHI for HMDB0003361 (Pyrimidine)

InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3-DiazinChEBI
1,3-DiazineChEBI
m-DiazineChEBI
MetadiazineChEBI
PyrimidinChEBI
Pyrimidine baseChEBI
1,3-DiazabenzeneHMDB
MiazineHMDB
PYHMDB
PYRHMDB
Pyrimidine dimerHMDB
Chemical FormulaC4H4N2
Average Molecular Weight80.088
Monoisotopic Molecular Weight80.037448138
IUPAC Namepyrimidine
Traditional Namepyrimidine
CAS Registry Number25247-63-6
SMILES
C1=CN=CN=C1
InChI Identifier
InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
InChI KeyCZPWVGJYEJSRLH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidines and pyrimidine derivatives. Pyrimidines and pyrimidine derivatives are compounds containing a pyrimidne ring, which is a six-member aromatic heterocycle which consists of two nitrogen atoms (at positions 1 and 3) and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidines and pyrimidine derivatives
Alternative Parents
Substituents
  • Pyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point22 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 25 °CNot Available
LogP-0.40HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Campylobacter jejuni infection		 details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023153
KNApSAcK IDC00007494
Chemspider ID8903
KEGG Compound IDC00396
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPyrimidine
METLIN IDNot Available
PubChem Compound9260
PDB IDNot Available
ChEBI ID16898
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Loffler M, Fairbanks LD, Zameitat E, Marinaki AM, Simmonds HA: Pyrimidine pathways in health and disease. Trends Mol Med. 2005 Sep;11(9):430-7. [PubMed:16098809 ]

Enzymes

Enzyme Details
1. DNA damage-binding protein 2
General function:
Involved in damaged DNA binding
Specific function:
Required for DNA repair. Binds to DDB1 to form the UV- damaged DNA-binding protein complex (the UV-DDB complex). The UV- DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1- CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4- ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair
Gene Name:
DDB2
Uniprot ID:
Q92466
Molecular weight:
47863.5
Enzyme Details
2. DNA damage-binding protein 1
General function:
Involved in nucleic acid binding
Specific function:
Required for DNA repair. Binds to DDB2 to form the UV- damaged DNA-binding protein complex (the UV-DDB complex). The UV- DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin- protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2
Gene Name:
DDB1
Uniprot ID:
Q16531
Molecular weight:
126966.9
Enzyme Details
3. Poly(U)-binding-splicing factor PUF60
General function:
Involved in nucleotide binding
Specific function:
DNA- and RNA-binding protein, involved in several nuclear processes such as pre-mRNA splicing, apoptosis and transcription regulation. In association with FUBP1 regulates MYC transcription at the P2 promoter through the core-TFIIH basal transcription factor. Acts as a transcriptional repressor through the core-TFIIH basal transcription factor. Represses FUBP1-induced transcriptional activation but not basal transcription. Decreases ERCC3 helicase activity. Does not repress TFIIH-mediated transcription in xeroderma pigmentosum complementation group B (XPB) cells. Is also involved in pre-mRNA splicing. Promotes splicing of an intron with weak 3'-splice site and pyrimidine tract in a cooperative manner with U2AF2. Involved in apoptosis induction when overexpressed in HeLa cells. Isoform 6 failed to repress MYC transcription and inhibited FIR-induced apoptosis in colorectal cancer. Isoform 6 may contribute to tumor progression by enabling increased MYC expression and greater resistance to apoptosis in tumors than in normal cells. Modulates alternative splicing of several mRNAs. Binds to relaxed DNA of active promoter regions. Binds to the pyrimidine tract and 3'-splice site regions of pre-mRNA; binding is enhanced in presence of U2AF2. Binds to Y5 RNA in association with TROVE2. Binds to poly(U) RNA
Gene Name:
PUF60
Uniprot ID:
Q9UHX1
Molecular weight:
59875.0