Np mrd loader

Showing NP-Card for Purine (NP0000513)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:40:13 UTC
NP-MRD IDNP0000513
Secondary Accession NumbersNone
Natural Product Identification
Common NamePurine
DescriptionPurine, also known as purine base or 1H-purine, belongs to the class of organic compounds known as purines and purine derivatives. These are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring. Two of the bases in nucleic acids, adenine and guanine, are purines. Purines from food (or from tissue turnover) are metabolised by several enzymes, including xanthine oxidase, into uric acid. Purine exists in all living species, ranging from bacteria to humans. High levels of uric acid can predispose to gout when the acid crystalises in joints; this phenomenon only happens in humans and some animal species (e.G. Dogs) that lack an intrinsic uricase enzyme that can further degrade uric acid. In humans, purine is involved in thioguanine action pathway. Outside of the human body, purine is found, on average, in the highest concentration within cocoa beans. Purine has also been detected, but not quantified in several different foods, such as rapinis, plains prickly pears, blackcurrants, radish, and parsley. This could make purine a potential biomarker for the consumption of these foods. Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000513 (Purine)


  Mrv1652305271900272D          

  9 10  0  0  0  0            999 V2000
    0.1627    0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1627   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.6653    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5520    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9448   -0.6687    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5520   -0.8209    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4295    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2668    0.4105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2703   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  2  0  0  0  0
  6  9  2  0  0  0  0
  5  7  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for NP0000513 (Purine)

HMDB0001366
     RDKit          3D
Purine
 13 14  0  0  0  0  0  0  0  0999 V2000
   -2.3470   -0.5234   -0.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0636    0.7739    0.1397 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8125    1.2575    0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2502    0.3874    0.0619 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5868    0.5648    0.0825 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1506   -0.6361   -0.1177 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757   -1.5504   -0.2613 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0286   -0.9443   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3063   -1.3727   -0.2165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3650   -0.8542   -0.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5726    2.2982    0.3799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1065    1.4702    0.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2257   -0.8709   -0.1629 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

3D SDF for NP0000513 (Purine)


  Mrv1652305271900272D          

  9 10  0  0  0  0            999 V2000
    0.1627    0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1627   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483    0.6653    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5520    0.8244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9448   -0.6687    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5520   -0.8209    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4295    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2668    0.4105    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2703   -0.4105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  2  0  0  0  0
  6  9  2  0  0  0  0
  5  7  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000513

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N1C=NC2=C1C=NC=N2

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9)

> <INCHI_KEY>
KDCGOANMDULRCW-UHFFFAOYSA-N

> <FORMULA>
C5H4N4

> <MOLECULAR_WEIGHT>
120.1121

> <EXACT_MASS>
120.043596148

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.89537647246423

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7H-purine

> <ALOGPS_LOGP>
-0.19

> <JCHEM_LOGP>
-0.33900180666666646

> <ALOGPS_LOGS>
-0.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.310986074202647

> <JCHEM_PKA_STRONGEST_BASIC>
2.7601684440882974

> <JCHEM_POLAR_SURFACE_AREA>
54.46

> <JCHEM_REFRACTIVITY>
33.2056

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.35e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
purine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000513 (Purine)

HMDB0001366
     RDKit          3D
Purine
 13 14  0  0  0  0  0  0  0  0999 V2000
   -2.3470   -0.5234   -0.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0636    0.7739    0.1397 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8125    1.2575    0.2110 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2502    0.3874    0.0619 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5868    0.5648    0.0825 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1506   -0.6361   -0.1177 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1757   -1.5504   -0.2613 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0286   -0.9443   -0.1544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3063   -1.3727   -0.2165 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3650   -0.8542   -0.1187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5726    2.2982    0.3799 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1065    1.4702    0.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2257   -0.8709   -0.1629 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  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  1  1  0
  8  4  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
M  END
Download

PDB for NP0000513 (Purine)

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  C   UNK     0       0.304   0.766   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.304  -0.766   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.770   1.242   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -1.030   1.539   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       1.764  -1.248   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      -1.030  -1.532   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.668   0.000   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -2.365   0.766   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -2.371  -0.766   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    7                                                       
CONECT    6    2    9                                                       
CONECT    7    3    5                                                       
CONECT    8    4    9                                                       
CONECT    9    6    8                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
Download

3D PDB for NP0000513 (Purine)

COMPND    HMDB0001366
HETATM    1  C1  UNL     1      -2.347  -0.523  -0.071  1.00  0.00           C  
HETATM    2  N1  UNL     1      -2.064   0.774   0.140  1.00  0.00           N  
HETATM    3  C2  UNL     1      -0.813   1.257   0.211  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.250   0.387   0.062  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.587   0.565   0.082  1.00  0.00           N  
HETATM    6  C4  UNL     1       2.151  -0.636  -0.118  1.00  0.00           C  
HETATM    7  N3  UNL     1       1.176  -1.550  -0.261  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.029  -0.944  -0.154  1.00  0.00           C  
HETATM    9  N4  UNL     1      -1.306  -1.373  -0.217  1.00  0.00           N  
HETATM   10  H1  UNL     1      -3.365  -0.854  -0.119  1.00  0.00           H  
HETATM   11  H2  UNL     1      -0.573   2.298   0.380  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.107   1.470   0.227  1.00  0.00           H  
HETATM   13  H4  UNL     1       3.226  -0.871  -0.163  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3
CONECT    3    4    4   11
CONECT    4    5    8
CONECT    5    6   12
CONECT    6    7    7   13
CONECT    7    8
CONECT    8    9    9
END
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SMILES for NP0000513 (Purine)

N1C=NC2=C1C=NC=N2
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INCHI for NP0000513 (Purine)

InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9)
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View in JSmol
Synonyms
ValueSource
Purine baseChEBI
1H-PurineHMDB
6H-Imidazo[4,5-D]pyrimidineHMDB
7-MethyltheophyllineHMDB
7H-Imidazo(4,5-D)pyrimidineHMDB
7H-PurineHMDB
9H-PurineHMDB
beta-PurineHMDB
CaffedrineHMDB
CaffeinHMDB
CafipelHMDB
CoffeineHMDB
DasinHMDB
DexitacHMDB
DiurexHMDB
DurvitanHMDB
Imidazo(4,5-D)pyrimidineHMDB
IsopurineHMDB
KoffeinHMDB
MateinaHMDB
MethyltheobromineHMDB
PhensalHMDB
Propoxyphene compound 65HMDB
{6h-imidazo[4,5-D]pyrimidine}HMDB
{7h-imidazo[4,} 5-D]pyrimidineHMDB
{Imidazo[4,5-D]pyrimidine}HMDB
Chemical FormulaC5H4N4
Average Mass120.1121 Da
Monoisotopic Mass120.04360 Da
IUPAC Name7H-purine
Traditional Namepurine
CAS Registry Number120-73-0
SMILES
N1C=NC2=C1C=NC=N2
InChI Identifier
InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9)
InChI KeyKDCGOANMDULRCW-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 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
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)Varshavi.d262021-08-01View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Arabidopsis thalianaKNApSAcK Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dolichos lablabKNApSAcK Database
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Homo sapiensLOTUS Database
Humulus lupulusKNApSAcK Database
Ipomoea batatasKNApSAcK Database
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Mangifera indicaKNApSAcK Database
Medicago sativaKNApSAcK Database
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Mercurialis ambiguaKNApSAcK Database
Nicotiana tabacumKNApSAcK Database
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Oryza sativaKNApSAcK Database
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Pisum sativumKNApSAcK Database
Solanum tuberosumKNApSAcK Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Theobroma cacaoFooDB
Species Where Detected
Species NameSourceReference
Agrobacterium tumefaciensKNApSAcK Database
Corynebacterium fasciansKNApSAcK Database
Ecklonia maximaKNApSAcK Database
Euglena gracilisKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as purines and purine derivatives. These are aromatic heterocyclic compounds containing a purine moiety, which is formed a pyrimidine-ring ring fused to an imidazole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct ParentPurines and purine derivatives
Alternative Parents
Substituents
  • Purine
  • Pyrimidine
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point214 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility500 mg/mLNot Available
LogP-0.37Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility53.5 g/LALOGPS
logP-0.19ALOGPS
logP-0.34ChemAxon
logS-0.35ALOGPS
pKa (Strongest Acidic)9.31ChemAxon
pKa (Strongest Basic)2.76ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.46 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.21 m³·mol⁻¹ChemAxon
Polarizability10.9 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001366
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB007311
KNApSAcK IDC00000095
Chemspider ID1015
KEGG Compound IDC15587
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPurine
METLIN ID6193
PubChem Compound1044
PDB IDNot Available
ChEBI ID17258
Good Scents IDrw1279341
References
General References
  1. Gudbjornsson B, Zak A, Niklasson F, Hallgren R: Hypoxanthine, xanthine, and urate in synovial fluid from patients with inflammatory arthritides. Ann Rheum Dis. 1991 Oct;50(10):669-72. [PubMed:1958086 ]
  2. Yamamoto T, Moriwaki Y, Cheng J, Takahashi S, Tsutsumi Z, Ka T, Hada T: Effect of inosine on the plasma concentration of uridine and purine bases. Metabolism. 2002 Apr;51(4):438-42. [PubMed:11912550 ]
  3. van Os S, de Abreu R, Hopman J, Wethly K, Liem D, van de Bor M: Purine and pyrimidine metabolism and electrocortical brain activity during hypoxemia in near-term lambs. Pediatr Res. 2004 Jun;55(6):1018-25. Epub 2004 Mar 17. [PubMed:15028845 ]
  4. Yegutkin GG, Samburski SS, Jalkanen S: Soluble purine-converting enzymes circulate in human blood and regulate extracellular ATP level via counteracting pyrophosphatase and phosphotransfer reactions. FASEB J. 2003 Jul;17(10):1328-30. Epub 2003 May 20. [PubMed:12759341 ]
  5. Nakashima K, Inoue K, Mayahara K, Kuroda N, Hamachi Y, Akiyama S: Use of 3-(1,8-naphthalimido)propyl-modified silyl silica gel as a stationary phase for the high-performance liquid chromatographic separation of purine derivatives. J Chromatogr A. 1996 Jan 26;722(1-2):107-13. [PubMed:9019292 ]
  6. Schmidt H, Siems WG, Grune T, Grauel EL: Concentration of purine compounds in the cerebrospinal fluid of infants suffering from sepsis, convulsions and hydrocephalus. J Perinat Med. 1995;23(3):167-74. [PubMed:8568608 ]
  7. Lyoo IK, Demopulos CM, Hirashima F, Ahn KH, Renshaw PF: Oral choline decreases brain purine levels in lithium-treated subjects with rapid-cycling bipolar disorder: a double-blind trial using proton and lithium magnetic resonance spectroscopy. Bipolar Disord. 2003 Aug;5(4):300-6. [PubMed:12895208 ]
  8. Burnstock G: Purine-mediated signalling in pain and visceral perception. Trends Pharmacol Sci. 2001 Apr;22(4):182-8. [PubMed:11282418 ]
  9. Witte DP, Wiginton DA, Hutton JJ, Aronow BJ: Coordinate developmental regulation of purine catabolic enzyme expression in gastrointestinal and postimplantation reproductive tracts. J Cell Biol. 1991 Oct;115(1):179-90. [PubMed:1918135 ]
  10. Shore PM, Jackson EK, Wisniewski SR, Clark RS, Adelson PD, Kochanek PM: Vascular endothelial growth factor is increased in cerebrospinal fluid after traumatic brain injury in infants and children. Neurosurgery. 2004 Mar;54(3):605-11; discussion 611-2. [PubMed:15028134 ]