Showing NP-Card for Xanthine (NP0000734)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2022-02-09 15:59:40 UTC
NP-MRD IDNP0000734
Secondary Accession NumbersNone
Natural Product Identification
Common NameXanthine
DescriptionXanthine, also known as 2,6-dioxopurine, belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety. Xanthine is also classified as an oxopurine. An oxopurine in which the purine ring is substituted by oxo groups at positions 2 and 6 and N-9 is protonated. Xanthine exists in all living species, ranging from bacteria to plants to humans. In plants, several stimulants can be derived from xanthine, including caffeine, theophylline, and theobromine. Derivatives of xanthine (known collectively as xanthines) are a group of alkaloids commonly used for their effects as mild stimulants and as bronchodilators, notably in the treatment of asthma or influenza symptoms. Within humans, xanthine participates in a number of enzymatic reactions. In particular, xanthine can be biosynthesized from guanine; which is mediated by the enzyme guanine deaminase. In addition, xanthine and ribose 1-phosphate can be biosynthesized from xanthosine through the action of the enzyme purine nucleoside phosphorylase. In humans and other primates, xanthine can be converted to uric acid by the action of the xanthine oxidase enzyme. People with rare genetic disorders, specifically xanthinuria and Lesch–Nyhan syndrome, lack sufficient xanthine oxidase and cannot convert xanthine to uric acid. Individuals with xanthinuria have unusually high concentrations of xanthine in their blood and urine, which can lead to health problems such as renal failure and xanthine kidney stones. Individuals with Lesch-Nyhan syndrome have a deficiency of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT). The HGPRT deficiency causes a build-up of uric acid in all body fluids. This results in both high levels of uric acid in the blood and urine, associated with severe gout and kidney problems. Neurological signs include poor muscle control and moderate intellectual disability.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000734 (Xanthine)

 
  Mrv1652309042000002D          

 11 12  0  0  0  0            999 V2000
   14.2313   -9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2313  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4888   -9.2400    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738  -10.7250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4888  -10.5600    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.6750   -9.4875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738   -8.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9938   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6750  -10.2712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4175  -10.6837    0.0000 O   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
  3  8  2  0  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6  9  2  0  0  0  0
  7 10  1  0  0  0  0
M  END
Download

3D MOL for NP0000734 (Xanthine)

HMDB0000292
     RDKit          3D
Xanthine
 15 16  0  0  0  0  0  0  0  0999 V2000
   -3.2608   -0.6489    0.1356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0318   -0.3213    0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7301    0.9667    0.2053 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4297    1.3458    0.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1665    2.5720    0.2719 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5787    0.4163    0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9079    0.4767   -0.0695 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4253   -0.7714   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3845   -1.6464   -0.2530 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2515   -0.9221   -0.1093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0598   -1.2255   -0.0591 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4980    1.6651    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4796    1.3539   -0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4697   -1.0301   -0.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3205   -2.2309   -0.1453 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11  2  1  0
 10  6  2  0
  3 12  1  0
  7 13  1  0
  8 14  1  0
 11 15  1  0
M  END
Download

3D SDF for NP0000734 (Xanthine)

 
  Mrv1652309042000002D          

 11 12  0  0  0  0            999 V2000
   14.2313   -9.4875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2313  -10.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4888   -9.2400    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738  -10.7250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.4888  -10.5600    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.6750   -9.4875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.9738   -8.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.9938   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6750  -10.2712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4175  -10.6837    0.0000 O   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
  3  8  2  0  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6  9  2  0  0  0  0
  7 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000734

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1NC2=C(NC=N2)C(=O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)

> <INCHI_KEY>
LRFVTYWOQMYALW-UHFFFAOYSA-N

> <FORMULA>
C5H4N4O2

> <MOLECULAR_WEIGHT>
152.1109

> <EXACT_MASS>
152.033425392

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.702109770186718

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,6,7-tetrahydro-1H-purine-2,6-dione

> <ALOGPS_LOGP>
-0.65

> <JCHEM_LOGP>
-0.20706379166666647

> <ALOGPS_LOGS>
-1.49

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.765949537699065

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.954237880526347

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7029128013721097

> <JCHEM_POLAR_SURFACE_AREA>
86.88

> <JCHEM_REFRACTIVITY>
36.9219

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.91e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
xanthine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000734 (Xanthine)

HMDB0000292
     RDKit          3D
Xanthine
 15 16  0  0  0  0  0  0  0  0999 V2000
   -3.2608   -0.6489    0.1356 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0318   -0.3213    0.0929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7301    0.9667    0.2053 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4297    1.3458    0.1634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1665    2.5720    0.2719 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5787    0.4163    0.0066 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9079    0.4767   -0.0695 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4253   -0.7714   -0.2284 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3845   -1.6464   -0.2530 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2515   -0.9221   -0.1093 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0598   -1.2255   -0.0591 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4980    1.6651    0.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4796    1.3539   -0.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4697   -1.0301   -0.3193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3205   -2.2309   -0.1453 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11  2  1  0
 10  6  2  0
  3 12  1  0
  7 13  1  0
  8 14  1  0
 11 15  1  0
M  END
Download

PDB for NP0000734 (Xanthine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      26.565 -17.710   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.565 -19.250   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.951 -16.940   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      25.179 -17.248   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      27.951 -20.020   0.000  0.00  0.00           N+0
HETATM    6  N   UNK     0      25.179 -19.712   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0      29.260 -17.710   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0      27.951 -15.400   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      24.255 -18.480   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      29.260 -19.173   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      30.646 -19.943   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10                                                       
CONECT    6    2    9                                                       
CONECT    7    3   10                                                       
CONECT    8    3                                                            
CONECT    9    4    6                                                       
CONECT   10    5   11    7                                                  
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for NP0000734 (Xanthine)

COMPND    HMDB0000292
HETATM    1  O1  UNL     1      -3.261  -0.649   0.136  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.032  -0.321   0.093  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.730   0.967   0.205  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.430   1.346   0.163  1.00  0.00           C  
HETATM    5  O2  UNL     1      -0.167   2.572   0.272  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.579   0.416   0.007  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.908   0.477  -0.069  1.00  0.00           N  
HETATM    8  C4  UNL     1       2.425  -0.771  -0.228  1.00  0.00           C  
HETATM    9  N3  UNL     1       1.385  -1.646  -0.253  1.00  0.00           N  
HETATM   10  C5  UNL     1       0.252  -0.922  -0.109  1.00  0.00           C  
HETATM   11  N4  UNL     1      -1.060  -1.225  -0.059  1.00  0.00           N  
HETATM   12  H1  UNL     1      -2.498   1.665   0.324  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.480   1.354  -0.016  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.470  -1.030  -0.319  1.00  0.00           H  
HETATM   15  H4  UNL     1      -1.321  -2.231  -0.145  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   11
CONECT    3    4   12
CONECT    4    5    5    6
CONECT    6    7   10   10
CONECT    7    8   13
CONECT    8    9    9   14
CONECT    9   10
CONECT   10   11
CONECT   11   15
END
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SMILES for NP0000734 (Xanthine)

O=C1NC2=C(NC=N2)C(=O)N1
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INCHI for NP0000734 (Xanthine)

InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
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View in JSmol
Synonyms
Chemical FormulaC5H4N4O2
Average Mass152.1109 Da
Monoisotopic Mass152.03343 Da
IUPAC Name2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Namexanthine
CAS Registry Number69-89-6
SMILES
O=C1NC2=C(NC=N2)C(=O)N1
InChI Identifier
InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
InChI KeyLRFVTYWOQMYALW-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-02-09View Spectrum
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, 100%_DMSO, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Bos taurus domesticusKNApSAcK Database
Escherichia coli K12KNApSAcK Database
Homo sapiens (Serum)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as xanthines. These are purine derivatives with a ketone group conjugated at carbons 2 and 6 of the purine moiety.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct ParentXanthines
Alternative Parents
Substituents
  • Xanthine
  • 6-oxopurine
  • Purinone
  • Alkaloid or derivatives
  • Pyrimidone
  • Pyrimidine
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Vinylogous amide
  • Lactam
  • Urea
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.069 mg/mL at 16 °C; 9.5 mg/mL (sodium salt)Maynard, R. L. (1997). The Merck Index: 1996. Occupational and Environmental Medicine, 54(4), 288.
LogP-0.73Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility4.91 g/LALOGPS
logP-0.65ALOGPS
logP-0.21ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)7.95ChemAxon
pKa (Strongest Basic)-0.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.88 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity36.92 m³·mol⁻¹ChemAxon
Polarizability12.7 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000292
DrugBank IDDB02134
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001977
KNApSAcK IDC00019660
Chemspider ID1151
KEGG Compound IDC00385
BioCyc IDXANTHINE
BiGG ID34825
Wikipedia LinkXanthine
METLIN ID82
PubChem Compound1188
PDB IDNot Available
ChEBI ID17712
Good Scents IDrw1297041
References
General References