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Showing metabocard for 3-Hydroxyhexanoic acid (HMDB0061652)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2014-04-11 22:16:54 UTC
Update Date2021-09-14 15:45:32 UTC
HMDB IDHMDB0061652
Secondary Accession Numbers
  • HMDB61652
Metabolite Identification
Common Name3-Hydroxyhexanoic acid
Description3-Hydroxyhexanoic acid, also known as (S)-3-hydroxycaproic acid or 3-hydroxycaproate, belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain. Based on a literature review a significant number of articles have been published on 3-Hydroxyhexanoic acid.
Structure
Data?1571930751
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061652 (3-Hydroxyhexanoic acid)

  Mrv1652310241917202D          

  9  8  0  0  0  0            999 V2000
 9997.9637 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9998.4815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5339 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1042 9998.0698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6785 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3942 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
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3D MOL for HMDB0061652 (3-Hydroxyhexanoic acid)

HMDB0061652
     RDKit          3D
3-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.7519    0.0733   -0.2971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6440    1.0390   -0.0299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2919    0.5851   -0.5319 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1693   -0.6902    0.0614 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3044   -0.6534    1.4472 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4951   -1.0880   -0.5085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5923   -0.1360   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7140   -0.4562   -0.8002 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5524    1.0383    0.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6855    0.5686   -0.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5172   -0.7333   -0.9881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0808   -0.3616    0.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8798    1.9882   -0.5596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5739    1.2866    1.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3496    0.4488   -1.6330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4104    1.3954   -0.2852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5275   -1.5418   -0.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8897   -1.4177    1.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8381   -2.0739   -0.0906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -1.1873   -1.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9623    1.9162    0.0794 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  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  0
  3 16  1  0
  4 17  1  1
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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3D SDF for HMDB0061652 (3-Hydroxyhexanoic acid)

  Mrv1652310241917202D          

  9  8  0  0  0  0            999 V2000
 9997.9637 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9998.4815    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.5339 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.1042 9998.0698    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8190 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2489 9999.3071    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6785 9998.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.3942 9998.0698    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  0  0  0  0
  2  3  1  0  0  0  0
  2  7  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061652

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1

> <INCHI_KEY>
HPMGFDVTYHWBAG-YFKPBYRVSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.159

> <EXACT_MASS>
132.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.870107740812344

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3-hydroxyhexanoic acid

> <ALOGPS_LOGP>
0.57

> <JCHEM_LOGP>
0.5800850606666665

> <ALOGPS_LOGS>
0.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.288991049395367

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.67423988970905

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7983718893851792

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.589099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.33e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-3-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0061652 (3-Hydroxyhexanoic acid)

HMDB0061652
     RDKit          3D
3-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.7519    0.0733   -0.2971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6440    1.0390   -0.0299 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2919    0.5851   -0.5319 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1693   -0.6902    0.0614 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3044   -0.6534    1.4472 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4951   -1.0880   -0.5085 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5923   -0.1360   -0.2796 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7140   -0.4562   -0.8002 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5524    1.0383    0.4187 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6855    0.5686   -0.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5172   -0.7333   -0.9881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0808   -0.3616    0.6914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8798    1.9882   -0.5596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5739    1.2866    1.0525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3496    0.4488   -1.6330 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4104    1.3954   -0.2852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5275   -1.5418   -0.1611 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8897   -1.4177    1.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8381   -2.0739   -0.0906 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3740   -1.1873   -1.6292 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9623    1.9162    0.0794 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  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  0
  3 16  1  0
  4 17  1  1
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for HMDB0061652 (3-Hydroxyhexanoic acid)

HEADER    PROTEIN                                 24-OCT-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-OCT-19         0                                  
HETATM    1  C   UNK     0    8662.8668663.064   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8661.5318663.832   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8660.1978663.064   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8658.8628663.832   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0    8657.5288663.064   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8658.8628665.373   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8661.5318665.373   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.2008663.832   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8665.5368663.064   0.000  0.00  0.00           C+0
CONECT    1    2    8                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2                                                            
CONECT    8    1    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0061652 (3-Hydroxyhexanoic acid)

COMPND    HMDB0061652
HETATM    1  C1  UNL     1      -2.752   0.073  -0.297  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.644   1.039  -0.030  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.292   0.585  -0.532  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.169  -0.690   0.061  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.304  -0.653   1.447  1.00  0.00           O  
HETATM    6  C5  UNL     1       1.495  -1.088  -0.509  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.592  -0.136  -0.280  1.00  0.00           C  
HETATM    8  O2  UNL     1       3.714  -0.456  -0.800  1.00  0.00           O  
HETATM    9  O3  UNL     1       2.552   1.038   0.419  1.00  0.00           O  
HETATM   10  H1  UNL     1      -3.686   0.569  -0.682  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.517  -0.733  -0.988  1.00  0.00           H  
HETATM   12  H3  UNL     1      -3.081  -0.362   0.691  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.880   1.988  -0.560  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.574   1.287   1.053  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.350   0.449  -1.633  1.00  0.00           H  
HETATM   16  H7  UNL     1       0.410   1.395  -0.285  1.00  0.00           H  
HETATM   17  H8  UNL     1      -0.527  -1.542  -0.161  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.890  -1.418   1.679  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.838  -2.074  -0.091  1.00  0.00           H  
HETATM   20  H11 UNL     1       1.374  -1.187  -1.629  1.00  0.00           H  
HETATM   21  H12 UNL     1       2.962   1.916   0.079  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5    6   17
CONECT    5   18
CONECT    6    7   19   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for HMDB0061652 (3-Hydroxyhexanoic acid)

CCC[C@H](O)CC(O)=O
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INCHI for HMDB0061652 (3-Hydroxyhexanoic acid)

InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC6H12O3
Average Molecular Weight132.159
Monoisotopic Molecular Weight132.078644246
IUPAC Name(3S)-3-hydroxyhexanoic acid
Traditional Name(S)-3-hydroxyhexanoic acid
CAS Registry Number66997-60-2
SMILES
CCC[C@H](O)CC(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-2-3-5(7)4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1
InChI KeyHPMGFDVTYHWBAG-YFKPBYRVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassMedium-chain hydroxy acids and derivatives
Direct ParentMedium-chain hydroxy acids and derivatives
Alternative Parents
Substituents
  • Medium-chain hydroxy acid
  • Medium-chain fatty acid
  • Beta-hydroxy acid
  • Hydroxy fatty acid
  • Fatty acyl
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
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
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified20 uMAdult (>18 years old)MaleNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified6-510 uMChildren (1-13 years old)Male3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Metastatic melanoma		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency
  1. Thompson GN, Hsu BY, Pitt JJ, Treacy E, Stanley CA: Fasting hypoketotic coma in a child with deficiency of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase. N Engl J Med. 1997 Oct 23;337(17):1203-7. doi: 10.1056/NEJM199710233371704. [PubMed:9337379 ]
Metastatic melanoma
  1. Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY: Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia. 2017 Oct;19(10):848-855. doi: 10.1016/j.neo.2017.08.004. Epub 2017 Sep 15. [PubMed:28923537 ]
Associated OMIM IDs
  • 605911 (3-Hydroxy-3-Methylglutaryl-CoA Synthase Deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10004129
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11829482
PDB IDNot Available
ChEBI ID37049
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 References
  1. Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
  2. The AOCS Lipid Library [Link]