Hmdb loader

Showing metabocard for 2-Hydroxy-3-methylpentanoic acid (HMDB0000317)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-05-30 20:55:49 UTC
HMDB IDHMDB0000317
Secondary Accession Numbers
  • HMDB00317
Metabolite Identification
Common Name2-Hydroxy-3-methylpentanoic acid
Description2-Hydroxy-3-methylpentanoic acid or 2-hydroxy-3-methylvaleric acid (HMVA) is an organic acid generated by L-isoleucine metabolism. It is derived from the reduction of 2-Keto-3-methylvaleric acid (KMVA), possibly through the action of a lactate dehydrogenase (PMID: 1429566 ). There are 4 stereoisomers of HMVA (2S,3S-HMVA, 2R,3R-HMVA, 2S,3R-HMVA and 2R,3S-HMVA), of which the 2S,3S and 2S,3R derivatives are generally separable. HMVA is found in the urine and blood of normal individuals but in very elevated levels in patients with maple syrup urine disease (MSUD) (PMID: 1429566 ). Maple syrup urine disease (MSUD) is an inherited metabolic disease predominantly characterized by neurological dysfunction including psychomotor/delay/mental retardation.
Structure
Data?1676999682
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)


  Mrv0541 02231218272D          

  9  8  0  0  1  0            999 V2000
   15.9718  -14.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4007  -13.5066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -12.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2574  -13.0941    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5428  -13.5066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9718  -13.5066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2574  -12.2690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8283  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)

HMDB0000317
     RDKit          3D
2-Hydroxy-3-methylpentanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.3245    0.2406    0.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8206    0.5497    0.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.0291   -0.5178 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3857   -1.4578   -0.6647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1375    0.5531   -0.7843 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6098    0.0124   -2.0070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0858    0.2855    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1389   -0.3676    0.0882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8207    0.7577    1.5752 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    1.0660    1.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238    0.0124   -0.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5139   -0.6625    1.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.6524    0.8045 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3908    0.0744    1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8815    0.4634   -1.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3169   -1.7043   -1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.7235   -0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4127   -2.0389   -0.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365    1.6529   -0.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -0.9068   -1.8826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271    1.5120    1.9036 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)


  Mrv0541 02231218272D          

  9  8  0  0  1  0            999 V2000
   15.9718  -14.3316    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.4007  -13.5066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -12.2690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.2574  -13.0941    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.5428  -13.5066    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9718  -13.5066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.2574  -12.2690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8283  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6863  -13.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  1  1  6  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  4  7  1  1  0  0  0
  5  8  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000317

> <DATABASE_NAME>
hmdb

> <SMILES>
CC[C@@H](C)[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1

> <INCHI_KEY>
RILPIWOPNGRASR-RFZPGFLSSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.773780943384981

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2-hydroxy-3-methylpentanoic acid

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
0.8602343683333333

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.044948135264622

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.25405925572059

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8957913795351873

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.4364

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-methyl-valerate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)

HMDB0000317
     RDKit          3D
2-Hydroxy-3-methylpentanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
    2.3245    0.2406    0.8271 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8206    0.5497    0.7645 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.0291   -0.5178 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3857   -1.4578   -0.6647 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1375    0.5531   -0.7843 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6098    0.0124   -2.0070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0858    0.2855    0.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1389   -0.3676    0.0882 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8207    0.7577    1.5752 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8955    1.0660    1.2606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7238    0.0124   -0.1871 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5139   -0.6625    1.4414 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.6524    0.8045 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3908    0.0744    1.6717 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8815    0.4634   -1.3397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3169   -1.7043   -1.7470 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028   -1.7235   -0.3463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4127   -2.0389   -0.1651 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0365    1.6529   -0.9951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9410   -0.9068   -1.8826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271    1.5120    1.9036 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
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

PDB for HMDB0000317 (2-Hydroxy-3-methylpentanoic 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      29.814 -26.752   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      32.481 -25.212   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      31.148 -22.902   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      28.480 -24.442   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      27.147 -25.212   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      29.814 -25.212   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.480 -22.902   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.813 -24.442   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.148 -24.442   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    5    6    7                                                  
CONECT    5    4    8                                                       
CONECT    6    1    4    9                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    2    3    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)

COMPND    HMDB0000317
HETATM    1  C1  UNL     1       2.324   0.241   0.827  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.821   0.550   0.764  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.232   0.029  -0.518  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.386  -1.458  -0.665  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.138   0.553  -0.784  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.610   0.012  -2.007  1.00  0.00           O  
HETATM    7  C6  UNL     1      -2.086   0.285   0.300  1.00  0.00           C  
HETATM    8  O2  UNL     1      -3.139  -0.368   0.088  1.00  0.00           O  
HETATM    9  O3  UNL     1      -1.821   0.758   1.575  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.895   1.066   1.261  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.724   0.012  -0.187  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.514  -0.662   1.441  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.722   1.652   0.805  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.391   0.074   1.672  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.882   0.463  -1.340  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.317  -1.704  -1.747  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.403  -1.723  -0.346  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.413  -2.039  -0.165  1.00  0.00           H  
HETATM   19  H10 UNL     1      -1.037   1.653  -0.995  1.00  0.00           H  
HETATM   20  H11 UNL     1      -1.941  -0.907  -1.883  1.00  0.00           H  
HETATM   21  H12 UNL     1      -2.427   1.512   1.904  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    5   15
CONECT    4   16   17   18
CONECT    5    6    7   19
CONECT    6   20
CONECT    7    8    8    9
CONECT    9   21
END
Download

SMILES for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)

CC[C@@H](C)[C@@H](O)C(O)=O
Download

INCHI for HMDB0000317 (2-Hydroxy-3-methylpentanoic acid)

InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-3-methylpentanoateGenerator
(2R,3R)-2-Hydroxy-3-methyl-pentanoateHMDB
(2R,3R)-2-Hydroxy-3-methyl-pentanoic acidHMDB
(2R,3R)-2-Hydroxy-3-methylpentanoateHMDB
(2R,3R)-2-Hydroxy-3-methylpentanoic acidHMDB
2-Hydroxy-3-methyl-pentanoateHMDB
2-Hydroxy-3-methyl-pentanoic acidHMDB
2-Hydroxy-3-methyl-valerateHMDB
2-Hydroxy-3-methyl-valeric acidHMDB
2-Hydroxy-3-methylvalerateHMDB
2-Hydroxy-3-methylvaleric acidHMDB
a-Hydroxy-b-methylvalerateHMDB
a-Hydroxy-b-methylvaleric acidHMDB
alpha-Hydroxy-beta-methylvalerateHMDB
alpha-Hydroxy-beta-methylvaleric acidHMDB
HMVAHMDB
Chemical FormulaC6H12O3
Average Molecular Weight132.1577
Monoisotopic Molecular Weight132.07864425
IUPAC Name(2R,3R)-2-hydroxy-3-methylpentanoic acid
Traditional Name2-hydroxy-3-methyl-valerate
CAS Registry Number488-15-3
SMILES
CC[C@@H](C)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)/t4-,5-/m1/s1
InChI KeyRILPIWOPNGRASR-RFZPGFLSSA-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 effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
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
PropertyValueSource
Water Solubility149 g/LALOGPS
logP0.74ALOGPS
logP0.86ChemAxon
logS0.05ALOGPS
pKa (Strongest Acidic)4.25ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability13.77 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+129.80431661259
DarkChem[M-H]-124.95231661259
AllCCS[M+H]+132.4932859911
AllCCS[M-H]-128.9332859911
DeepCCS[M+H]+129.77630932474
DeepCCS[M-H]-126.25430932474
DeepCCS[M-2H]-163.42330932474
DeepCCS[M+Na]+138.90830932474
AllCCS[M+H]+132.532859911
AllCCS[M+H-H2O]+128.432859911
AllCCS[M+NH4]+136.332859911
AllCCS[M+Na]+137.532859911
AllCCS[M-H]-128.932859911
AllCCS[M+Na-2H]-131.732859911
AllCCS[M+HCOO]-134.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.15 minutes32390414
Predicted by Siyang on May 30, 202210.7283 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.27 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid89.0 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1286.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid354.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid97.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid206.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid83.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid378.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid403.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)99.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid753.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid322.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1040.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid234.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid297.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate405.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA278.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water140.1 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Hydroxy-3-methylpentanoic acidCC[C@@H](C)[C@@H](O)C(O)=O2006.4Standard polar33892256
2-Hydroxy-3-methylpentanoic acidCC[C@@H](C)[C@@H](O)C(O)=O1083.2Standard non polar33892256
2-Hydroxy-3-methylpentanoic acidCC[C@@H](C)[C@@H](O)C(O)=O1153.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Hydroxy-3-methylpentanoic acid,1TMS,isomer #1CC[C@@H](C)[C@@H](O[Si](C)(C)C)C(=O)O1208.1Semi standard non polar33892256
2-Hydroxy-3-methylpentanoic acid,1TMS,isomer #2CC[C@@H](C)[C@@H](O)C(=O)O[Si](C)(C)C1143.4Semi standard non polar33892256
2-Hydroxy-3-methylpentanoic acid,2TMS,isomer #1CC[C@@H](C)[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C1259.7Semi standard non polar33892256
2-Hydroxy-3-methylpentanoic acid,1TBDMS,isomer #1CC[C@@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O1443.3Semi standard non polar33892256
2-Hydroxy-3-methylpentanoic acid,1TBDMS,isomer #2CC[C@@H](C)[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C1364.2Semi standard non polar33892256
2-Hydroxy-3-methylpentanoic acid,2TBDMS,isomer #1CC[C@@H](C)[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C1708.3Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified<0.7 uMNewborn (0-30 days old)Not SpecifiedNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified<0.7 uMNewborn (0-30 days old)Not SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
UrineDetected and Quantified6.531 +/- 5.519 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Normal
    • Analysis of 30 no...
 details
UrineDetected and Quantified0.0 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified3.9 (1.7-7.9) umol/mmol creatinineAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.04 (0.02-0.06) umol/mmol creatinineNewborn (0-30 days old)Both
Normal
    • Analysis of 40 NI...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified46.6 uMNewborn (0-30 days old)FemaleMaple syrup urine disease details
Cerebrospinal Fluid (CSF)Detected and Quantified17 uMNewborn (0-30 days old)FemaleMaple syrup urine disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn disease		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)MaleTooth Decay details
UrineDetected but not QuantifiedNot QuantifiedNot AvailableNot AvailableMaple syrup urine disease (MSUD) details
UrineDetected but not QuantifiedNot QuantifiedNot AvailableNot AvailableDihydrolipoyl DH (E3) deficiency details
UrineDetected and Quantified13.765 +/- 12.068 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
Eosinophilic esophagitis
    • Analysis of 30 no...
 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 ]
Crohn's disease
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Ulcerative colitis
  1. Azario I, Pievani A, Del Priore F, Antolini L, Santi L, Corsi A, Cardinale L, Sawamoto K, Kubaski F, Gentner B, Bernardo ME, Valsecchi MG, Riminucci M, Tomatsu S, Aiuti A, Biondi A, Serafini M: Neonatal umbilical cord blood transplantation halts skeletal disease progression in the murine model of MPS-I. Sci Rep. 2017 Aug 25;7(1):9473. doi: 10.1038/s41598-017-09958-9. [PubMed:28842642 ]
Tooth Decay
  1. Liebsch C, Pitchika V, Pink C, Samietz S, Kastenmuller G, Artati A, Suhre K, Adamski J, Nauck M, Volzke H, Friedrich N, Kocher T, Holtfreter B, Pietzner M: The Saliva Metabolome in Association to Oral Health Status. J Dent Res. 2019 Jun;98(6):642-651. doi: 10.1177/0022034519842853. Epub 2019 Apr 26. [PubMed:31026179 ]
Maple syrup urine disease
  1. Kumps A, Duez P, Mardens Y: Metabolic, nutritional, iatrogenic, and artifactual sources of urinary organic acids: a comprehensive table. Clin Chem. 2002 May;48(5):708-17. [PubMed:11978597 ]
  2. Shigematsu Y, Kikuchi K, Momoi T, Sudo M, Kikawa Y, Nosaka K, Kuriyama M, Haruki S, Sanada K, Hamano N, et al.: Organic acids and branched-chain amino acids in body fluids before and after multiple exchange transfusions in maple syrup urine disease. J Inherit Metab Dis. 1983;6(4):183-9. [PubMed:6422161 ]
Dihydrolipoamide Dehydrogenase Deficiency
  1. Kumps A, Duez P, Mardens Y: Metabolic, nutritional, iatrogenic, and artifactual sources of urinary organic acids: a comprehensive table. Clin Chem. 2002 May;48(5):708-17. [PubMed:11978597 ]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021944
KNApSAcK IDC00052119
Chemspider ID8972081
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5306
PubChem Compound10796774
PDB IDNot Available
ChEBI ID89228
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMamer, O.A. & Reimer, M.L.J. "On the Mechanisms of the Formation of L-Alloisoleucine and the 2-Hydroxy-3-methylvaleric Acid.." J. Biol. Chem. 267: 22141-22147 (1992).
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Mamer OA, Reimer ML: On the mechanisms of the formation of L-alloisoleucine and the 2-hydroxy-3-methylvaleric acid stereoisomers from L-isoleucine in maple syrup urine disease patients and in normal humans. J Biol Chem. 1992 Nov 5;267(31):22141-7. [PubMed:1429566 ]