MiMeDB: Showing metabocard for 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (MMDBc0031760)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:48:12 UTC

Update Date

2022-08-31 18:24:26 UTC

Metabolite ID

MMDBc0031760

Metabolite Identification

Common Name

5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate

Description

5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate is an intermediate in purine degradataion. It is a byproduct of 5-hydroxyisurate metabolism. It is generated by the enzyme hydroxyisourate hydrolase which catalyzes the reaction 5-hydroxyisourate + H2O <=> 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate. In most organisms, including some bacteria (such as E. coli), plants, and certain animals, urate is metabolized via a common pathway, producing the stereospecific form S-allantoin as the final product. In the first step of the pathway factor-independent urate hydroxylase catalyzes the conversion of urate to 5-hydroxyisourate. 5-hydroxyisourate is relatively unstable, and often decomposes in vitro to yield racemic allantoin. Hydroxyisourate hydrolase catalyzes the hydrolysis of the N1-C6 bond of 5-hydroxyisourate to form 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H imidazole-5-carboxylate.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309042000402D          

 14 14  0  0  0  0            999 V2000
    0.4520    2.3766    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3182    2.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    1.2571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219    1.0435    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9712    1.7354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0532    2.4555    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7452    2.0061    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7020    1.1823    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    0.8077    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3939    0.7329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7951    1.7786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2750    2.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4601    3.2793    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9669    3.3541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  5  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  9  3  1  0  0  0  0
  3  2  1  0  0  0  0
  6  2  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  5 11  2  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031760

> <DATABASE_NAME>
MIME

> <SMILES>
NC(=O)NC1=NC(=O)NC1(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H6N4O5/c6-3(12)7-1-5(14,2(10)11)9-4(13)8-1/h14H,(H,10,11)(H4,6,7,8,9,12,13)

> <INCHI_KEY>
WHKYNCPIXMNTRQ-UHFFFAOYSA-N

> <FORMULA>
C5H6N4O5

> <MOLECULAR_WEIGHT>
202.1249

> <EXACT_MASS>
202.033819322

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
16.004617959627303

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(carbamoylamino)-5-hydroxy-2-oxo-2,5-dihydro-1H-imidazole-5-carboxylic acid

> <ALOGPS_LOGP>
-1.86

> <JCHEM_LOGP>
-2.2777762976666662

> <ALOGPS_LOGS>
-1.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.332369787461557

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5311433200394338

> <JCHEM_PKA_STRONGEST_BASIC>
-1.1180337776917915

> <JCHEM_POLAR_SURFACE_AREA>
154.10999999999999

> <JCHEM_REFRACTIVITY>
38.66830000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.85e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(carbamoylamino)-4-hydroxy-2-oxo-3H-imidazole-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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  N   UNK     0       0.844   4.436   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.594   3.884   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.513   2.347   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.974   1.948   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       1.813   3.239   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.966   4.584   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -3.258   3.745   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -3.177   2.207   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.805   1.508   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0      -4.469   1.368   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.351   3.320   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.513   5.422   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.859   6.121   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.805   6.261   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    6   12                                             
CONECT    3    4    9    2                                                  
CONECT    4    3    5                                                       
CONECT    5    1    4   11                                                  
CONECT    6    2                                                            
CONECT    7    8                                                            
CONECT    8    7    9   10                                                  
CONECT    9    3    8                                                       
CONECT   10    8                                                            
CONECT   11    5                                                            
CONECT   12    2   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
2-oxo-4-Hydroxy-4-carboxy-5-ureidoimidazoline	Kegg
5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylic acid	Generator

Molecular Formula

C₅H₆N₄O₅

Average Mass

202.1249

Monoisotopic Mass

202.033819322

IUPAC Name

4-(carbamoylamino)-5-hydroxy-2-oxo-2,5-dihydro-1H-imidazole-5-carboxylic acid

Traditional Name

5-(carbamoylamino)-4-hydroxy-2-oxo-3H-imidazole-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

NC(=O)NC1=NC(=O)NC1(O)C(O)=O

InChI Identifier

InChI=1S/C5H6N4O5/c6-3(12)7-1-5(14,2(10)11)9-4(13)8-1/h14H,(H,10,11)(H4,6,7,8,9,12,13)

InChI Key

WHKYNCPIXMNTRQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Alpha-hydroxy acid
Hydroxy acid
3-imidazoline
Carbonic acid derivative
Urea
Alkanolamine
Amidine
Carboxylic acid amidine
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

ureidocarboxylic acid (CHEBI:31132 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	4.85 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.3	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	2.53	ChemAxon
pKa (Strongest Basic)	-1.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	154.11 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	38.67 m³·mol⁻¹	ChemAxon
Polarizability	16 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fu-6900000000-d10ae3e6c0ec2b2ce715	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-004i-3091000000-2d5a8154318d1c851aeb	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ik9-1930000000-aa0ce54956d155b53ae0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-1900000000-4b7e4cde80ee20857785	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006x-9000000000-b47e099fd673e89bef01	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0a4l-1900000000-ada3c5b0af634149d258	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07vi-7900000000-8cfac7d8a2916a662122	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-000x-9000000000-87b0901f8a0972ac01f0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0290000000-6aef2ea3d16e64f66e0a	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0gw3-0920000000-77d0905884a3fca8fd7d	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-11c7af77cb066557a541	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0690000000-81226e034d27b996a665	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-3900000000-6c8214de7999a22c4230	2021-10-21	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-04fd0d084ea29b98bee7	2021-10-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0008299	5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate	Allantoin	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	45	Human feces; Human stool; Human ; Human feces; pleural fluid plaque; bal; Pig	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	114	Human feces; Human ; Human saliva	Metabolic reconstruction
Bacteria	Actinobacteria	17	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	1		Metabolic reconstruction
Bacteria	Bacteroidetes	43	Human feces; Human stool; Human saliva; Human ; Human gastric fluid; Human urine	Metabolic reconstruction
Bacteria	Fusobacteria	13	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Bacteria	Deinococcus-thermus	1
Eukaryota/Fungi	Ascomycota	1
Archaea/Archaea	Euryarchaeota	2		Metabolic reconstruction

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference
Plant		Glycine max	FooDB	24285751

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0301917

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB001617

KNApSAcK ID

Not Available

Chemspider ID

391844

KEGG Compound ID

C12248

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443736

PDB ID

Not Available

ChEBI ID

31132

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5-Hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (MMDBc0031760)

MOL for #<Metabolite:0x0000556b6729a798>

3D MOL for #<Metabolite:0x0000556b6729a798>

3D SDF for #<Metabolite:0x0000556b6729a798>

3D-SDF for #<Metabolite:0x0000556b6729a798>

PDB for #<Metabolite:0x0000556b6729a798>

3D PDB for #<Metabolite:0x0000556b6729a798>

SMILES for #<Metabolite:0x0000556b6729a798>

INCHI for #<Metabolite:0x0000556b6729a798>

Structure for #<Metabolite:0x0000556b6729a798>

3D Structure for #<Metabolite:0x0000556b6729a798>