Showing NP-Card for 7-Methylxanthine (NP0000525)

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Record Information
Version2.0
Created at2006-05-22 14:17:30 UTC
Updated at2025-02-11 15:42:02 UTC
NP-MRD IDNP0000525
Secondary Accession NumbersNone
Natural Product Identification
Common Name7-Methylxanthine
Description7-Methylxanthine is a methyl derivative of xanthine, found occasionally in human urine. 7-Methylxanthine is one of the purine components in urinary calculi. Methylated purines originate from the metabolism of methylxanthines (caffeine, theophylline and theobromine). Caffeine is metabolized via successive pathways mainly catalyzed by CYP1A2, xanthine oxidase or N-acetyltransferase-2 to give 14 different metabolites, including 7-methylxanthine. CYP1A2 activity shows an inter-individual variability among the population. CYP1A2, an isoform of the CYP1A cytochrome P450 super-family, is involved in the metabolism of many drugs and plays a potentially important role in the induction of chemical carcinogenesis. Purine derivatives in urinary calculi could be considered markers of abnormal purine metabolism. The content of a purine derivative in stone depends on its average urinary excretion in the general population, similarity to the chemical structure of uric acid, and content of the latter in stone. This suggests that purines in stones represent a solid solution with uric acid as solvent. It is also plausible that methylxanthines, ubiquitous components of the diet and drugs, are involved in the pathogenesis of urolithiasis. (PMID: 11712316 , 15833286 , 3506820 , 15013152 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000525 (7-Methylxanthine)

  Mrv1652309042000262D          

 12 13  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
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3D MOL for NP0000525 (7-Methylxanthine)

HMDB0001991
     RDKit          3D
7-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    1.6606   -0.7646    1.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0569    0.2430    0.9649 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3290    1.5544    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313    2.1069   -0.0353 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2693    1.1579   -0.5668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2359    1.1424   -1.5045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9021    0.0295   -1.8621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026    0.0759   -2.7515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.1216   -1.2456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6171   -1.1522   -0.3006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2951   -2.2276    0.2948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.0140    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3990   -0.2553    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8960   -1.2740    2.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2097   -1.5306    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0929    2.0267    1.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4865    2.0207   -1.9786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0626   -2.0175   -1.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12  2  1  0
 12  5  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  6 17  1  0
  9 18  1  0
M  END
Download

3D SDF for NP0000525 (7-Methylxanthine)

  Mrv1652309042000262D          

 12 13  0  0  0  0            999 V2000
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000525

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1C=NC2=C1C(=O)NC(=O)N2

> <INCHI_IDENTIFIER>
InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)

> <INCHI_KEY>
PFWLFWPASULGAN-UHFFFAOYSA-N

> <FORMULA>
C6H6N4O2

> <MOLECULAR_WEIGHT>
166.1374

> <EXACT_MASS>
166.049075456

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
14.765580625668878

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
0.01661227400000012

> <ALOGPS_LOGS>
-1.38

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.734120976934491

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.307899146071083

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8497959946108037

> <JCHEM_POLAR_SURFACE_AREA>
76.02000000000001

> <JCHEM_REFRACTIVITY>
41.818599999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-methylxanthine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000525 (7-Methylxanthine)

HMDB0001991
     RDKit          3D
7-Methylxanthine
 18 19  0  0  0  0  0  0  0  0999 V2000
    1.6606   -0.7646    1.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0569    0.2430    0.9649 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3290    1.5544    0.8866 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5313    2.1069   -0.0353 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2693    1.1579   -0.5668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2359    1.1424   -1.5045 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9021    0.0295   -1.8621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8026    0.0759   -2.7515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.1216   -1.2456 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6171   -1.1522   -0.3006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2951   -2.2276    0.2948 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0746   -0.0140    0.0752 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3990   -0.2553    2.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8960   -1.2740    2.4327 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2097   -1.5306    1.2493 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0929    2.0267    1.5071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4865    2.0207   -1.9786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0626   -2.0175   -1.4823 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12  2  1  0
 12  5  2  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  3 16  1  0
  6 17  1  0
  9 18  1  0
M  END
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PDB for NP0000525 (7-Methylxanthine)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.198  -2.843   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    2    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    5                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for NP0000525 (7-Methylxanthine)

COMPND    HMDB0001991
HETATM    1  C1  UNL     1       1.661  -0.765   1.817  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.057   0.243   0.965  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.329   1.554   0.887  1.00  0.00           C  
HETATM    4  N2  UNL     1       0.531   2.107  -0.035  1.00  0.00           N  
HETATM    5  C3  UNL     1      -0.269   1.158  -0.567  1.00  0.00           C  
HETATM    6  N3  UNL     1      -1.236   1.142  -1.504  1.00  0.00           N  
HETATM    7  C4  UNL     1      -1.902   0.029  -1.862  1.00  0.00           C  
HETATM    8  O1  UNL     1      -2.803   0.076  -2.752  1.00  0.00           O  
HETATM    9  N4  UNL     1      -1.579  -1.122  -1.246  1.00  0.00           N  
HETATM   10  C5  UNL     1      -0.617  -1.152  -0.301  1.00  0.00           C  
HETATM   11  O2  UNL     1      -0.295  -2.228   0.295  1.00  0.00           O  
HETATM   12  C6  UNL     1       0.075  -0.014   0.075  1.00  0.00           C  
HETATM   13  H1  UNL     1       2.399  -0.255   2.500  1.00  0.00           H  
HETATM   14  H2  UNL     1       0.896  -1.274   2.433  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.210  -1.531   1.249  1.00  0.00           H  
HETATM   16  H4  UNL     1       2.093   2.027   1.507  1.00  0.00           H  
HETATM   17  H5  UNL     1      -1.486   2.021  -1.979  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.063  -2.018  -1.482  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   12
CONECT    3    4    4   16
CONECT    4    5
CONECT    5    6   12   12
CONECT    6    7   17
CONECT    7    8    8    9
CONECT    9   10   18
CONECT   10   11   11   12
END
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SMILES for NP0000525 (7-Methylxanthine)

CN1C=NC2=C1C(=O)NC(=O)N2
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INCHI for NP0000525 (7-Methylxanthine)

InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)
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View in JSmol
Synonyms
ValueSource
3,7-Dihydro-7-methyl-1H-purine-2,6-dioneChEBI
7-MethylxanthinChEBI
HeteroxanthinChEBI
HeteroxanthineChEBI
7-Methylxanthine, 7-(13)C-labeledHMDB
2,6-Dihydroxy-7-methylpurineHMDB
7-Methyl-3,7-dihydro-1H-purine-2,6-dioneHMDB
7-Methyl-7H-purine-2,6-diolHMDB
MethylxanthineHMDB
Chemical FormulaC6H6N4O2
Average Mass166.1374 Da
Monoisotopic Mass166.04908 Da
IUPAC Name7-methyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Name7-methylxanthine
CAS Registry Number552-62-5
SMILES
CN1C=NC2=C1C(=O)NC(=O)N2
InChI Identifier
InChI=1S/C6H6N4O2/c1-10-2-7-4-3(10)5(11)9-6(12)8-4/h2H,1H3,(H2,8,9,11,12)
InChI KeyPFWLFWPASULGAN-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, 5%_DMSO, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-10View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Urine)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
  • Alkaloid or derivatives
  • Hydroxypyrimidine
  • Pyrimidine
  • N-substituted imidazole
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen 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 Solubility18070 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.89Gaspari, F., Vigano, G., Orisio, S., Bonati, M., Livio, M., & Remuzzi, G. (1987). Aspirin prolongs bleeding time in uremia by a mechanism distinct from platelet cyclooxygenase inhibition. The Journal of clinical investigation, 79(6), 1788-1797.
Predicted Properties
PropertyValueSource
Water Solubility7 g/LALOGPS
logP-0.59ALOGPS
logP0.017ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)9.31ChemAxon
pKa (Strongest Basic)-0.85ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area76.02 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity41.82 m³·mol⁻¹ChemAxon
Polarizability14.77 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001991
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB001978
KNApSAcK IDC00007326
Chemspider ID61660
KEGG Compound IDC16353
BioCyc ID7-METHYLXANTHINE
BiGG IDNot Available
Wikipedia LinkXanthine
METLIN IDNot Available
PubChem Compound68374
PDB IDNot Available
ChEBI ID48991
Good Scents IDrw1214051
References
General References
  1. Safranow K, Machoy Z: Simultaneous determination of 16 purine derivatives in urinary calculi by gradient reversed-phase high-performance liquid chromatography with UV detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 May 25;819(2):229-35. [PubMed:15833286 ]
  2. Safranow K: [Identification and quantitation of purine derivatives in urinary calculi as markers of abnormal purine metabolism by using high-performance liquid chromatography (HPLC)]. Ann Acad Med Stetin. 2000;46:35-49. [PubMed:11712316 ]
  3. Ashihara H, Sano H, Crozier A: Caffeine and related purine alkaloids: biosynthesis, catabolism, function and genetic engineering. Phytochemistry. 2008 Feb;69(4):841-56. doi: 10.1016/j.phytochem.2007.10.029. Epub 2007 Dec 19. [PubMed:18068204 ]