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Showing metabocard for 3-ureido-isobutyrate (HMDB0304156)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-24 07:38:17 UTC
Update Date2022-09-22 18:34:37 UTC
HMDB IDHMDB0304156
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-ureido-isobutyrate
DescriptionUreidoisobutyric acid, also known as 3-ureidoisobutyrate or beta-uba, is a member of the class of compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group. Ureidoisobutyric acid is soluble (in water) and a weakly acidic compound (based on its pKa). Ureidoisobutyric acid can be found in a number of food items such as pili nut, breakfast cereal, bitter gourd, and scarlet bean, which makes ureidoisobutyric acid a potential biomarker for the consumption of these food products. Ureidoisobutyric acid can be found primarily in blood, cerebrospinal fluid (CSF), and urine. Ureidoisobutyric acid exists in all living organisms, ranging from bacteria to humans. In humans, ureidoisobutyric acid is involved in the pyrimidine metabolism. Ureidoisobutyric acid is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). Moreover, ureidoisobutyric acid is found to be associated with beta-ureidopropionase deficiency.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304156 (3-ureido-isobutyrate)

  Mrv0541 02231219192D          

 10  9  0  0  0  0            999 V2000
   15.3740   -4.1659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2316   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6605   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.1659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5173   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.9908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  2  0  0  0  0
  4  7  1  0  0  0  0
  4  9  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 10  1  0  0  0  0
M  END
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3D MOL for HMDB0304156 (3-ureido-isobutyrate)

HMDB0304156
     RDKit          3D
3-ureido-isobutyrate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.3940   -0.3966    0.8946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2874   -0.4570   -0.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493   -0.2671    0.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1523   -0.3084   -0.3827 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4570   -0.1398    0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6014   -0.1711   -0.7016 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6131    0.0370    1.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4946    0.7031   -1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7038    0.5907   -2.2817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4591    1.9832   -0.5230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2105    0.5485    1.4719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3591   -0.2579    0.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3841   -1.2788    1.5610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3816   -1.4209   -0.6493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0871    0.6488    1.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1665   -1.1255    1.2324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0576   -0.4557   -1.4194 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0440    0.7029   -1.0753 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9802   -1.1142   -0.9390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5342    2.1787    0.4490 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  6 18  1  0
  6 19  1  0
 10 20  1  0
M  END
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3D SDF for HMDB0304156 (3-ureido-isobutyrate)

  Mrv0541 02231219192D          

 10  9  0  0  0  0            999 V2000
   15.3740   -4.1659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2316   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6605   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.1659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5173   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.9908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  2  0  0  0  0
  4  7  1  0  0  0  0
  4  9  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304156

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(CNC(N)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)

> <INCHI_KEY>
PHENTZNALBMCQD-UHFFFAOYSA-N

> <FORMULA>
C5H10N2O3

> <MOLECULAR_WEIGHT>
146.1445

> <EXACT_MASS>
146.069142196

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.810642910847072

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(carbamoylamino)-2-methylpropanoic acid

> <ALOGPS_LOGP>
-0.86

> <JCHEM_LOGP>
-0.882175473

> <ALOGPS_LOGS>
-0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.22016214605836

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3229374248469945

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7588206273546954

> <JCHEM_POLAR_SURFACE_AREA>
92.41999999999999

> <JCHEM_REFRACTIVITY>
33.3978

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-ureidoisobutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304156 (3-ureido-isobutyrate)

HMDB0304156
     RDKit          3D
3-ureido-isobutyrate
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.3940   -0.3966    0.8946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2874   -0.4570   -0.1519 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0493   -0.2671    0.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1523   -0.3084   -0.3827 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4570   -0.1398    0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6014   -0.1711   -0.7016 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6131    0.0370    1.3748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4946    0.7031   -1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7038    0.5907   -2.2817 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4591    1.9832   -0.5230 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2105    0.5485    1.4719 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3591   -0.2579    0.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3841   -1.2788    1.5610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3816   -1.4209   -0.6493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0871    0.6488    1.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1665   -1.1255    1.2324 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0576   -0.4557   -1.4194 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0440    0.7029   -1.0753 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9802   -1.1142   -0.9390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5342    2.1787    0.4490 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  6 18  1  0
  6 19  1  0
 10 20  1  0
M  END
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PDB for HMDB0304156 (3-ureido-isobutyrate)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      28.698  -7.776   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      35.366  -5.466   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      30.032  -5.466   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      34.032  -7.776   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      36.700  -7.776   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      31.365  -7.776   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      32.699  -7.006   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      31.365  -9.316   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      35.366  -7.006   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.032  -7.006   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4    7    9                                                       
CONECT    5    9                                                            
CONECT    6    7    8   10                                                  
CONECT    7    4    6                                                       
CONECT    8    6                                                            
CONECT    9    2    4    5                                                  
CONECT   10    1    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0304156 (3-ureido-isobutyrate)

COMPND    HMDB0304156
HETATM    1  C1  UNL     1      -2.394  -0.397   0.895  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.287  -0.457  -0.152  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.049  -0.267   0.523  1.00  0.00           C  
HETATM    4  N1  UNL     1       1.152  -0.308  -0.383  1.00  0.00           N  
HETATM    5  C4  UNL     1       2.457  -0.140   0.153  1.00  0.00           C  
HETATM    6  N2  UNL     1       3.601  -0.171  -0.702  1.00  0.00           N  
HETATM    7  O1  UNL     1       2.613   0.037   1.375  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.495   0.703  -1.050  1.00  0.00           C  
HETATM    9  O2  UNL     1      -1.704   0.591  -2.282  1.00  0.00           O  
HETATM   10  O3  UNL     1      -1.459   1.983  -0.523  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.211   0.549   1.472  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.359  -0.258   0.377  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.384  -1.279   1.561  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.382  -1.421  -0.649  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.087   0.649   1.137  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.167  -1.126   1.232  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.058  -0.456  -1.419  1.00  0.00           H  
HETATM   18  H8  UNL     1       4.044   0.703  -1.075  1.00  0.00           H  
HETATM   19  H9  UNL     1       3.980  -1.114  -0.939  1.00  0.00           H  
HETATM   20  H10 UNL     1      -1.534   2.179   0.449  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    8   14
CONECT    3    4   15   16
CONECT    4    5   17
CONECT    5    6    7    7
CONECT    6   18   19
CONECT    8    9    9   10
CONECT   10   20
END
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SMILES for HMDB0304156 (3-ureido-isobutyrate)

CC(CNC(N)=O)C(O)=O
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INCHI for HMDB0304156 (3-ureido-isobutyrate)

InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)
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Synonyms
Chemical FormulaC5H10N2O3
Average Molecular Weight146.1445
Monoisotopic Molecular Weight146.069142196
IUPAC Name3-(carbamoylamino)-2-methylpropanoic acid
Traditional Nameβ-ureidoisobutyric acid
CAS Registry NumberNot Available
SMILES
CC(CNC(N)=O)C(O)=O
InChI Identifier
InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)
InChI KeyPHENTZNALBMCQD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassUreas
Direct ParentUreas
Alternative Parents
Substituents
  • Urea
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030465
KNApSAcK IDNot Available
Chemspider ID141172
KEGG Compound IDC05100
BioCyc ID3-UREIDO-ISOBUTYRATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID1670
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available