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Showing metabocard for 2-Hydroxyvaleric acid (HMDB0001863)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-02-23 10:30:31 UTC
Update Date2023-02-21 17:15:51 UTC
HMDB IDHMDB0001863
Secondary Accession Numbers
  • HMDB01863
Metabolite Identification
Common Name2-Hydroxyvaleric acid
Description2-Hydroxyvaleric acid is an organic acid present in human biofluids. Its presence in urine has been associated with lactic acidosis, which occurs in Succinic Acidemia (OMIM 600335 ), a syndrome of organic acidemia associated with congenital lactic acidosis and decreased NADH-cytochrome c reductase activity. 2-Hydroxyvaleric acid presence associated with lactic acidosis has also been found in Propionyl-CoA carboxylase deficiency (OMIM 253260 ), or Multiple carboxylase deficiency (MCD), an autosomal recessive metabolic disorder characterized primarily by cutaneous and neurologic abnormalities. (PMID: 9389332 , 1790187 , 3378323 , 3383430 , 7313494 ).
Structure
Data?1676999751
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001863 (2-Hydroxyvaleric acid)

  Mrv0541 02231219142D          

  8  7  0  0  0  0            999 V2000
   17.8875   -4.9871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3163   -4.1622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6020   -2.9247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1730   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4585   -4.1622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8875   -4.1622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7441   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6020   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  8  1  0  0  0  0
  3  8  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for HMDB0001863 (2-Hydroxyvaleric acid)

HMDB0001863
     RDKit          3D
2-Hydroxyvaleric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5179   -0.6479    0.3145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1224   -0.1171    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3631    0.2177   -0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0104    0.7495   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606    1.0429   -1.5322 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9149   -0.1268    0.4223 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5791   -0.5304    1.5646 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1471   -0.5584   -0.0430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0035    0.0087   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0928   -0.6244    1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3904   -1.6708   -0.0882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3144    0.7603    1.3334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6947   -0.8996    1.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3795   -0.6681   -1.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9353    1.0097   -1.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9039    1.7212    0.2238 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2762    1.7838   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221   -1.4503   -0.4520 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
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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3D SDF for HMDB0001863 (2-Hydroxyvaleric acid)

  Mrv0541 02231219142D          

  8  7  0  0  0  0            999 V2000
   17.8875   -4.9871    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3163   -4.1622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6020   -2.9247    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1730   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4585   -4.1622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8875   -4.1622    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7441   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.6020   -3.7497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  8  1  0  0  0  0
  3  8  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001863

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCC(O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c1-2-3-4(6)5(7)8/h4,6H,2-3H2,1H3,(H,7,8)

> <INCHI_KEY>
JRHWHSJDIILJAT-UHFFFAOYSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.834773660076316

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxypentanoic acid

> <ALOGPS_LOGP>
0.26

> <JCHEM_LOGP>
0.49526154199999994

> <ALOGPS_LOGS>
0.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.284641269964371

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.1421099451224626

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7973131043245454

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
27.9648

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentanoic acid, 2-hydroxy-

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001863 (2-Hydroxyvaleric acid)

HMDB0001863
     RDKit          3D
2-Hydroxyvaleric acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.5179   -0.6479    0.3145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1224   -0.1171    0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3631    0.2177   -0.5540 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0104    0.7495   -0.3262 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606    1.0429   -1.5322 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9149   -0.1268    0.4223 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5791   -0.5304    1.5646 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1471   -0.5584   -0.0430 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0035    0.0087   -0.4311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0928   -0.6244    1.2669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3904   -1.6708   -0.0882 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3144    0.7603    1.3334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6947   -0.8996    1.3120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3795   -0.6681   -1.2275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9353    1.0097   -1.0945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9039    1.7212    0.2238 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2762    1.7838   -1.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221   -1.4503   -0.4520 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
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  8 18  1  0
M  END
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PDB for HMDB0001863 (2-Hydroxyvaleric acid)

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      33.390  -9.309   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      36.057  -7.770   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      34.724  -5.459   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      32.056  -6.999   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      30.723  -7.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      33.390  -7.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      29.389  -6.999   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      34.724  -6.999   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    8                                                            
CONECT    3    8                                                            
CONECT    4    5    6                                                       
CONECT    5    4    7                                                       
CONECT    6    1    4    8                                                  
CONECT    7    5                                                            
CONECT    8    2    3    6                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0001863 (2-Hydroxyvaleric acid)

COMPND    HMDB0001863
HETATM    1  C1  UNL     1      -2.518  -0.648   0.314  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.122  -0.117   0.678  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.363   0.218  -0.554  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.010   0.750  -0.326  1.00  0.00           C  
HETATM    5  O1  UNL     1       1.661   1.043  -1.532  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.915  -0.127   0.422  1.00  0.00           C  
HETATM    7  O2  UNL     1       1.579  -0.530   1.565  1.00  0.00           O  
HETATM    8  O3  UNL     1       3.147  -0.558  -0.043  1.00  0.00           O  
HETATM    9  H1  UNL     1      -3.004   0.009  -0.431  1.00  0.00           H  
HETATM   10  H2  UNL     1      -3.093  -0.624   1.267  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.390  -1.671  -0.088  1.00  0.00           H  
HETATM   12  H4  UNL     1      -1.314   0.760   1.333  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.695  -0.900   1.312  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.380  -0.668  -1.227  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.935   1.010  -1.094  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.904   1.721   0.224  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.276   1.784  -1.367  1.00  0.00           H  
HETATM   18  H10 UNL     1       3.322  -1.450  -0.452  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4   14   15
CONECT    4    5    6   16
CONECT    5   17
CONECT    6    7    7    8
CONECT    8   18
END
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SMILES for HMDB0001863 (2-Hydroxyvaleric acid)

CCCC(O)C(O)=O
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INCHI for HMDB0001863 (2-Hydroxyvaleric acid)

InChI=1S/C5H10O3/c1-2-3-4(6)5(7)8/h4,6H,2-3H2,1H3,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC5H10O3
Average Molecular Weight118.1311
Monoisotopic Molecular Weight118.062994186
IUPAC Name2-hydroxypentanoic acid
Traditional Namepentanoic acid, 2-hydroxy-
CAS Registry Number617-31-2
SMILES
CCCC(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-2-3-4(6)5(7)8/h4,6H,2-3H2,1H3,(H,7,8)
InChI KeyJRHWHSJDIILJAT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Monosaccharide
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point34 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP0.45SANGSTER (1993)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
FecesDetected but not QuantifiedNot QuantifiedInfant (0-1 year old)Both
Normal		 details
UrineDetected and Quantified0-4 umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
UrineDetected and Quantified0.1 +/- 0.1 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022717
KNApSAcK IDNot Available
Chemspider ID88482
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound98009
PDB IDNot Available
ChEBI ID60647
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceD'yakonov, I. A.; Vinogradova, N. B. Reactions of aliphatic diazo compounds with unsaturated compounds. VIII. Reaction of diazoacetic ester with allyl bromide. Zhurnal Obshchei Khimii (1951), 21 851-60.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Verhaeghe BJ, Lefevere MF, De Leenheer AP: Solid-phase extraction with strong anion-exchange columns for selective isolation and concentration of urinary organic acids. Clin Chem. 1988 Jun;34(6):1077-83. [PubMed:3378323 ]
  2. Bergstrom T, Greter J, Levin AH, Steen G, Tryding N, Wass U: Propionyl-CoA carboxylase deficiency: case report, effect of low-protein diet and identification of 3-oxo-2-methylvaleric acid 3-hydroxy-2-methylvaleric acid, and maleic acid in urine. Scand J Clin Lab Invest. 1981 Apr;41(2):117-26. [PubMed:7313494 ]
  3. Jellum E, Harboe M, Bjune G, Wold S: Interpreting complicated chromatographic patterns. J Pharm Biomed Anal. 1991;9(8):663-9. [PubMed:1790187 ]
  4. Kim KR, Kim JH, Jeong DH, Paek DJ, Liebich HM: Gas chromatographic profiling analysis of urinary organic acids from nonsmokers and smokers. J Chromatogr B Biomed Sci Appl. 1997 Nov 7;701(1):1-8. [PubMed:9389332 ]
  5. Asano K, Miyamoto I, Matsushita T, Murakami Y, Minoura S, Wagatsuma T, Oshima M: Succinic acidemia: a new syndrome of organic acidemia associated with congenital lactic acidosis and decreased NADH-cytochrome c reductase activity. Clin Chim Acta. 1988 Apr 29;173(3):305-12. [PubMed:3383430 ]

Enzymes

Enzyme Details
1. Sulfotransferase family cytosolic 2B member 1
General function:
Involved in sulfotransferase activity
Specific function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol.
Gene Name:
SULT2B1
Uniprot ID:
O00204
Molecular weight:
39598.595
Reactions
2-Hydroxyvaleric acid → 2-(sulfooxy)pentanoic aciddetails
Enzyme Details
2. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
2-Hydroxyvaleric acid → 6-(1-carboxybutoxy)-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
2-Hydroxyvaleric acid → 3,4,5-trihydroxy-6-[(2-hydroxypentanoyl)oxy]oxane-2-carboxylic aciddetails