Showing metabocard for Uric acid (MMDBc0000782)

Microbial
Human
Plant
Animal
Pharmaceutical
Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2020-12-10 18:54:49 UTC
Update Date2024-10-09 23:29:33 UTC
Metabolite IDMMDBc0000782
Metabolite Identification
Common NameUric acid
DescriptionUric acid is a heterocyclic purine derivative that is the final oxidation product of purine metabolism. It is a weak acid distributed throughout the extracellular fluid as sodium urate. Uric acid is produced by the enzyme xanthine oxidase, which oxidizes oxypurines such as xanthine into uric acid. In most mammals, except humans and higher primates, the enzyme uricase further oxidizes uric acid to allantoin. Interestingly, during the Miocene epoch (~15-20 million years ago), two distinct mutations in the primate genome occurred that led to a nonfunctioning uricase gene. Consequently, humans, apes, and certain New World monkeys have much higher uric acid levels (>120 μM) compared with other mammals (<<120 uM). The loss of uricase in higher primates parallels the similar loss of the ability to synthesize ascorbic acid vitamin C. This may be because in higher primates uric acid partially replaces ascorbic acid. Like ascorbic acid, uric acid is an antioxidant. In fact, in primates, uric acid is the major antioxidant in serum and is thought to be a major factor in lengthening life-span and decreasing age-specific cancer rates in humans and other primates (PMID: 6947260 ). Uric acid is also the end product of nitrogen metabolism in birds and reptiles. In these animal species, it is excreted in feces as a dry mass. In humans and other mammals, the amount of urate in the blood depends on the dietary intake of purines, the level of endogenous urate biosynthesis, and the rate of urate excretion. Several kidney urate transporters are involved in the regulation of plasma urate levels. These include the urate transporter 1 (URAT1), which controls the reabsorption of urate as well as a number of organic ion transporters (OAT), such as OAT1 and OAT3, and the ATP-dependent urate export transporter MRP4. URAT1 is believed to be most critical in the regulation of plasma urate levels. (PMID: 17890445 ) High levels of plasma uric acid lead to a condition called hyperuricemia while low levels are associated with a condition called hypouricemia. Hyperuricemia has been defined as a uric acid concentration greater than 380 μM, while hypouricemia is generally defined as a urate concentration of less than 120 μM. Hyperuricemia can arise from a number of factors, including both acute and chronic causes. Acute causes of hyperuricemia include the intake of large amounts of alcohol, tumor lysis syndrome and a diet that is rich in purines or proteins. Chronic hyperuricemia can arise from a reduction in the kidney’s glomerular filtration rate, a decrease in the excretion of urate or an increase in overall tubular absorption in the kidneys. Hyperuricemia has been linked to a number of diseases and conditions, including gout, hypertension, cardiovascular disease, myocardial infarction, stroke, and renal disease. Uric acid has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ). Many of the causes of hyperuricemia are correctable either with lifestyle changes or drugs. Lifestyle changes include reducing weight and reducing the consumption of protein, purines, and alcohol. There are two kinds of drugs that can be used to treat chronic hyperuricemia. Xanthine oxidase inhibitors, such as allopurinol, inhibit the production of urate by blocking urate synthesis. Alternately, uricosuric drugs, such as probenecid, sulfinpyrazone, and benzpromarone, are used to reduce the serum urate concentration through the inhibition of the URAT1 transporter. (PMID: 17890445 ). Uric acid (especially crystalline uric acid) is also thought to be an essential initiator and amplifier of allergic inflammation for asthma and peanut allergies (PMID: 21474346 ). 
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fade8ed0330>


  Mrv1652309042000002D          

 12 13  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  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
  6 12  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fade8ed0330>

HMDB0000289
     RDKit          3D
Uric acid
 16 17  0  0  0  0  0  0  0  0999 V2000
   -3.0705   -1.4091   -0.3526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9982   -0.7674   -0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1100    0.5558    0.0310 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9825    1.2560    0.1933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973    2.4897    0.4108 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2759    0.6766    0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5346    1.1267    0.2520 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4054    0.1204    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6734    0.1557    0.1475 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6648   -0.9940   -0.1241 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3588   -0.6813   -0.1105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7841   -1.3620   -0.2698 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0443    1.0316    0.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8046    2.1129    0.4377 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0787   -1.9250   -0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7095   -2.3867   -0.4511 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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12  2  1  0
 11  6  2  0
  3 13  1  0
  7 14  1  0
 10 15  1  0
 12 16  1  0
M  END
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3D SDF for #<Metabolite:0x00007fade8ed0330>


  Mrv1652309042000002D          

 12 13  0  0  0  0            999 V2000
    4.0668    2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -0.1271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  2  8  1  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
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000782

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)

> <INCHI_KEY>
LEHOTFFKMJEONL-UHFFFAOYSA-N

> <FORMULA>
C5H4N4O3

> <MOLECULAR_WEIGHT>
168.1103

> <EXACT_MASS>
168.028340014

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
13.613230919300054

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.12

> <JCHEM_LOGP>
-1.5441929356666664

> <ALOGPS_LOGS>
-1.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.972761778718843

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.246926773305706

> <JCHEM_PKA_STRONGEST_BASIC>
-6.523072814060841

> <JCHEM_POLAR_SURFACE_AREA>
99.33000000000001

> <JCHEM_REFRACTIVITY>
45.62859999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.76e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
uric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007fade8ed0330>

HMDB0000289
     RDKit          3D
Uric acid
 16 17  0  0  0  0  0  0  0  0999 V2000
   -3.0705   -1.4091   -0.3526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9982   -0.7674   -0.2027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1100    0.5558    0.0310 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9825    1.2560    0.1933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0973    2.4897    0.4108 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2759    0.6766    0.1303 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5346    1.1267    0.2520 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4054    0.1204    0.0999 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6734    0.1557    0.1475 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6648   -0.9940   -0.1241 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3588   -0.6813   -0.1105 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7841   -1.3620   -0.2698 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0443    1.0316    0.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8046    2.1129    0.4377 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0787   -1.9250   -0.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7095   -2.3867   -0.4511 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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12  2  1  0
 11  6  2  0
  3 13  1  0
  7 14  1  0
 10 15  1  0
 12 16  1  0
M  END
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PDB for #<Metabolite:0x00007fade8ed0330>

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  O   UNK     0       7.591   4.383   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.258   2.073   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.924  -0.237   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.924   4.383   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.320   2.843   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   12                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    2                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    6                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   26    0
END
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3D PDB for #<Metabolite:0x00007fade8ed0330>

COMPND    HMDB0000289
HETATM    1  O1  UNL     1      -3.070  -1.409  -0.353  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.998  -0.767  -0.203  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.110   0.556   0.031  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.982   1.256   0.193  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.097   2.490   0.411  1.00  0.00           O  
HETATM    6  C3  UNL     1       0.276   0.677   0.130  1.00  0.00           C  
HETATM    7  N2  UNL     1       1.535   1.127   0.252  1.00  0.00           N  
HETATM    8  C4  UNL     1       2.405   0.120   0.100  1.00  0.00           C  
HETATM    9  O3  UNL     1       3.673   0.156   0.147  1.00  0.00           O  
HETATM   10  N3  UNL     1       1.665  -0.994  -0.124  1.00  0.00           N  
HETATM   11  C5  UNL     1       0.359  -0.681  -0.111  1.00  0.00           C  
HETATM   12  N4  UNL     1      -0.784  -1.362  -0.270  1.00  0.00           N  
HETATM   13  H1  UNL     1      -3.044   1.032   0.086  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.805   2.113   0.438  1.00  0.00           H  
HETATM   15  H3  UNL     1       2.079  -1.925  -0.278  1.00  0.00           H  
HETATM   16  H4  UNL     1      -0.709  -2.387  -0.451  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   12
CONECT    3    4   13
CONECT    4    5    5    6
CONECT    6    7   11   11
CONECT    7    8   14
CONECT    8    9    9   10
CONECT   10   11   15
CONECT   11   12
CONECT   12   16
END
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SMILES for #<Metabolite:0x00007fade8ed0330>

O=C1NC2=C(N1)C(=O)NC(=O)N2
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INCHI for #<Metabolite:0x00007fade8ed0330>

InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
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Synonyms
ValueSource
2,6,8-TrioxopurineChEBI
2,6,8-TrioxypurineChEBI
Purine-2,6,8(1H,3H,9H)-trioneChEBI
UrateChEBI
1H-Purine-2,6,8-triolHMDB
2,6,8-TrihydroxypurineHMDB
LithateHMDB
Lithic acidHMDB
Acid urate, ammoniumHMDB
Ammonium acid urateHMDB
Monohydrate, sodium urateHMDB
Urate, ammonium acidHMDB
Urate, monosodiumHMDB
Acid, uricHMDB
Monosodium urate monohydrateHMDB
Sodium acid urateHMDB
Sodium urateHMDB
TrioxopurineHMDB
Urate, sodium acidHMDB
Monohydrate, monosodium urateHMDB
Monosodium urateHMDB
Potassium urateHMDB
Sodium acid urate monohydrateHMDB
Urate monohydrate, sodiumHMDB
Acid urate, sodiumHMDB
Sodium urate monohydrateHMDB
Urate monohydrate, monosodiumHMDB
Urate, potassiumHMDB
Urate, sodiumHMDB
Molecular FormulaC5H4N4O3
Average Mass168.1103
Monoisotopic Mass168.028340014
IUPAC Name2,3,6,7,8,9-hexahydro-1H-purine-2,6,8-trione
Traditional Nameuric acid
CAS Registry NumberNot Available
SMILES
O=C1NC2=C(N1)C(=O)NC(=O)N2
InChI Identifier
InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
InChI KeyLEHOTFFKMJEONL-UHFFFAOYSA-N