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Showing NP-Card for Pyrimidine (NP0000310)

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Record Information
Version1.0
Created at2006-08-12 19:21:07 UTC
Updated at2021-10-07 20:41:00 UTC
NP-MRD IDNP0000310
Secondary Accession NumbersNone
Natural Product 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000310 (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 NP0000310 (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
Download

3D SDF for NP0000310 (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>
NP0000310

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000310 (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
Download

PDB for NP0000310 (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 NP0000310 (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 NP0000310 (Pyrimidine)

C1=CN=CN=C1
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INCHI for NP0000310 (Pyrimidine)

InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H
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View in JSmol
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 Mass80.0880 Da
Monoisotopic Mass80.03745 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Daphnia magnaLOTUS Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiensLOTUS Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Species Where Detected
Species NameSourceReference
Bacillus subtilisKNApSAcK Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point22 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000 mg/mL at 25 °CNot Available
LogP-0.40Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility470 g/LALOGPS
logP-0.21ALOGPS
logP0.05ChemAxon
logS0.77ALOGPS
pKa (Strongest Basic)1.58ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area25.78 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity22.72 m³·mol⁻¹ChemAxon
Polarizability7.62 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0003361
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDNot Available
References
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 ]
  2. Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]
  3. Taneda S, Monnier VM: ELISA of pentosidine, an advanced glycation end product, in biological specimens. Clin Chem. 1994 Sep;40(9):1766-73. [PubMed:8070089 ]
  4. Bhurta D, Bharate SB: Analyzing the scaffold diversity of cyclin-dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Med Res Rev. 2021 Oct 4. doi: 10.1002/med.21856. [PubMed:34605036 ]
  5. Tsiko U, Bezvikonnyi O, Sych G, Keruckiene R, Volyniuk D, Simokaitiene J, Danyliv I, Danyliv Y, Bucinskas A, Tan X, Grazulevicius JV: Multifunctional derivatives of pyrimidine-5-carbonitrile and differently substituted carbazoles for doping-free sky-blue OLEDs and luminescent sensors of oxygen. J Adv Res. 2021 Feb 4;33:41-51. doi: 10.1016/j.jare.2021.01.014. eCollection 2021 Nov. [PubMed:34603777 ]