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Showing metabocard for 1-Methyluric acid (HMDB0003099)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 15:12:32 UTC
Update Date2023-02-21 17:16:32 UTC
HMDB IDHMDB0003099
Secondary Accession Numbers
  • HMDB03099
Metabolite Identification
Common Name1-Methyluric acid
Description1-Methyluric acid is one of the three main theophylline metabolites in man. 1-Methyluric acid is one of the purine components in urinary calculi. Methylated purines originate from the metabolism of methylxanthines (caffeine, theophylline, and theobromine). Methyluric acids can be distinguished from uric acid via simple methods routinely used in clinical laboratories, requiring the use of high-performance liquid chromatography (HPLC). 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. Caffeine is metabolized via successive pathways mainly catalyzed by CYP1A2, xanthine oxidase, or N-acetyltransferase-2 to give 14 different metabolites. CYP1A2 activity shows an inter-individual variability among the population. CYP1A2, an isoform of the CYP1A cytochrome P450 superfamily, is involved in the metabolism of many drugs and plays a potentially important role in the induction of chemical carcinogenesis (PMID:11712316 , 15833286 , 3506820 , 15013152 , 4039734 , 9890610 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003099 (1-Methyluric acid)

  Mrv1652309042000282D          

 13 14  0  0  0  0            999 V2000
    2.7845    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   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    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 O   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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  2  0  0  0  0
M  END
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3D MOL for HMDB0003099 (1-Methyluric acid)

HMDB0003099
     RDKit          3D
1-Methyluric acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.9923   -0.2113    0.0486 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5517    0.0573   -0.0077 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0729    1.2929   -0.2344 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106    2.2202   -0.3981 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2453    1.5764   -0.2928 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1822    0.6244   -0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5367    0.5958   -0.1272 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9390   -0.6796    0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1557   -1.0213    0.1576 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8363   -1.4079    0.2400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7231   -0.6568    0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6440   -0.9208    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0284   -2.1075    0.3821 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2737   -0.5626    1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5188    0.7201   -0.1560 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2108   -1.0422   -0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6026    2.5432   -0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1639    1.4280   -0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8182   -2.4483    0.4288 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12  2  1  0
 11  6  2  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  5 17  1  0
  7 18  1  0
 10 19  1  0
M  END
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3D SDF for HMDB0003099 (1-Methyluric acid)

  Mrv1652309042000282D          

 13 14  0  0  0  0            999 V2000
    2.7845    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -0.1271    0.0000 O   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    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    2.3479    0.0000 O   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
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  5 10  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0003099

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1C(=O)NC2=C(NC(=O)N2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H6N4O3/c1-10-4(11)2-3(9-6(10)13)8-5(12)7-2/h1H3,(H,9,13)(H2,7,8,12)

> <INCHI_KEY>
QFDRTQONISXGJA-UHFFFAOYSA-N

> <FORMULA>
C6H6N4O3

> <MOLECULAR_WEIGHT>
182.1368

> <EXACT_MASS>
182.043990078

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.725862137209987

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methyl-2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione

> <ALOGPS_LOGP>
-1.15

> <JCHEM_LOGP>
-1.32051687

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.880095047769107

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.671819121930137

> <JCHEM_PKA_STRONGEST_BASIC>
-6.168799154143619

> <JCHEM_POLAR_SURFACE_AREA>
90.54

> <JCHEM_REFRACTIVITY>
50.5253

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.23e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-methyluric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0003099 (1-Methyluric acid)

HMDB0003099
     RDKit          3D
1-Methyluric acid
 19 20  0  0  0  0  0  0  0  0999 V2000
    2.9923   -0.2113    0.0486 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5517    0.0573   -0.0077 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0729    1.2929   -0.2344 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9106    2.2202   -0.3981 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2453    1.5764   -0.2928 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1822    0.6244   -0.1251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5367    0.5958   -0.1272 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9390   -0.6796    0.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1557   -1.0213    0.1576 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8363   -1.4079    0.2400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7231   -0.6568    0.1097 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6440   -0.9208    0.1648 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0284   -2.1075    0.3821 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2737   -0.5626    1.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5188    0.7201   -0.1560 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2108   -1.0422   -0.6234 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6026    2.5432   -0.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1639    1.4280   -0.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8182   -2.4483    0.4288 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12  2  1  0
 11  6  2  0
  1 14  1  0
  1 15  1  0
  1 16  1  0
  5 17  1  0
  7 18  1  0
 10 19  1  0
M  END
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PDB for HMDB0003099 (1-Methyluric acid)

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       5.198   1.303   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.864   2.073   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.530  -0.237   0.000  0.00  0.00           O+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   3.613   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.713   2.843   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -0.268   1.597   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       2.530   4.383   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.198   4.383   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   10                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8    5                                                       
CONECT   11    6   12                                                       
CONECT   12   11    2   13                                                  
CONECT   13   12                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END
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3D PDB for HMDB0003099 (1-Methyluric acid)

COMPND    HMDB0003099
HETATM    1  C1  UNL     1       2.992  -0.211   0.049  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.552   0.057  -0.008  1.00  0.00           N  
HETATM    3  C2  UNL     1       1.073   1.293  -0.234  1.00  0.00           C  
HETATM    4  O1  UNL     1       1.911   2.220  -0.398  1.00  0.00           O  
HETATM    5  N2  UNL     1      -0.245   1.576  -0.293  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.182   0.624  -0.125  1.00  0.00           C  
HETATM    7  N3  UNL     1      -2.537   0.596  -0.127  1.00  0.00           N  
HETATM    8  C4  UNL     1      -2.939  -0.680   0.102  1.00  0.00           C  
HETATM    9  O2  UNL     1      -4.156  -1.021   0.158  1.00  0.00           O  
HETATM   10  N4  UNL     1      -1.836  -1.408   0.240  1.00  0.00           N  
HETATM   11  C5  UNL     1      -0.723  -0.657   0.110  1.00  0.00           C  
HETATM   12  C6  UNL     1       0.644  -0.921   0.165  1.00  0.00           C  
HETATM   13  O3  UNL     1       1.028  -2.107   0.382  1.00  0.00           O  
HETATM   14  H1  UNL     1       3.274  -0.563   1.083  1.00  0.00           H  
HETATM   15  H2  UNL     1       3.519   0.720  -0.156  1.00  0.00           H  
HETATM   16  H3  UNL     1       3.211  -1.042  -0.623  1.00  0.00           H  
HETATM   17  H4  UNL     1      -0.603   2.543  -0.470  1.00  0.00           H  
HETATM   18  H5  UNL     1      -3.164   1.428  -0.281  1.00  0.00           H  
HETATM   19  H6  UNL     1      -1.818  -2.448   0.429  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3   12
CONECT    3    4    4    5
CONECT    5    6   17
CONECT    6    7   11   11
CONECT    7    8   18
CONECT    8    9    9   10
CONECT   10   11   19
CONECT   11   12
CONECT   12   13   13
END
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SMILES for HMDB0003099 (1-Methyluric acid)

CN1C(=O)NC2=C(NC(=O)N2)C1=O
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INCHI for HMDB0003099 (1-Methyluric acid)

InChI=1S/C6H6N4O3/c1-10-4(11)2-3(9-6(10)13)8-5(12)7-2/h1H3,(H,9,13)(H2,7,8,12)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-MethylateGenerator
1-Methylic acidGenerator
1-MethylurateHMDB, MeSH
Chemical FormulaC6H6N4O3
Average Molecular Weight182.1368
Monoisotopic Molecular Weight182.043990078
IUPAC Name1-methyl-2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione
Traditional Name1-methyluric acid
CAS Registry Number708-79-2
SMILES
CN1C(=O)NC2=C(NC(=O)N2)C1=O
InChI Identifier
InChI=1S/C6H6N4O3/c1-10-4(11)2-3(9-6(10)13)8-5(12)7-2/h1H3,(H,9,13)(H2,7,8,12)
InChI KeyQFDRTQONISXGJA-UHFFFAOYSA-N
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
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility5 mg/mLNot Available
LogP-0.57GASPARI,F & BONATI,M (1987)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg129.17930932474
[M-H]-Not Available129.179http://allccs.zhulab.cn/database/detail?ID=AllCCS00000355
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Amniotic Fluid
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Kidney
  • Liver
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified7.04 +/- 1.57 umol/mmol creatinineAdult (>18 years old)BothCanavan disease details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal adenoma 		details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Canavan disease
  1. Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. [PubMed:16139832 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023107
KNApSAcK IDNot Available
Chemspider ID62926
KEGG Compound IDC16359
BioCyc IDCPD-14119
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID2821
PubChem Compound69726
PDB IDNot Available
ChEBI ID68441
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000410
Good Scents IDNot Available
References
Synthesis ReferencePrusse, August. Synthesis of methylated uric acids according to Behrend and Roosen. Ann. (1925), 441 203-15.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Xanthine dehydrogenase/oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Key enzyme in purine degradation. Catalyzes the oxidation of hypoxanthine to xanthine. Catalyzes the oxidation of xanthine to uric acid. Contributes to the generation of reactive oxygen species. Has also low oxidase activity towards aldehydes (in vitro).
Gene Name:
XDH
Uniprot ID:
P47989
Molecular weight:
146422.99
Reactions
1-Methylxanthine + Water + Oxygen → 1-Methyluric acid + Hydrogen peroxidedetails