Showing metabocard for 7-Methylxanthine (MMDBc0000399)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:36:53 UTC
Update Date2024-04-30 19:32:09 UTC
Metabolite IDMMDBc0000399
Metabolite 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fa4cd116498>


  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 #<Metabolite:0x00007fa4cd116498>

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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3D SDF for #<Metabolite:0x00007fa4cd116498>


  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>
MMDBc0000399

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007fa4cd116498>

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 #<Metabolite:0x00007fa4cd116498>

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 #<Metabolite:0x00007fa4cd116498>

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 #<Metabolite:0x00007fa4cd116498>

CN1C=NC2=C1C(=O)NC(=O)N2
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INCHI for #<Metabolite:0x00007fa4cd116498>

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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Synonyms
ValueSource
3,7-Dihydro-7-methyl-1H-purine-2,6-dioneChEBI
7-MethylxanthinChEBI
HeteroxanthinChEBI
HeteroxanthineChEBI
7-Methylxanthine, 7-(13)C-labeledMeSH
2,6-Dihydroxy-7-methylpurineHMDB
7-Methyl-3,7-dihydro-1H-purine-2,6-dioneHMDB
7-Methyl-7H-purine-2,6-diolHMDB
MethylxanthineHMDB
Molecular FormulaC6H6N4O2
Average Mass166.1374
Monoisotopic Mass166.049075456
IUPAC Name7-methyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione
Traditional Name7-methylxanthine
CAS Registry NumberNot Available
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