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Showing metabocard for 5-Hydroxyhexanoic acid (HMDB0000525)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:00:08 UTC
HMDB IDHMDB0000525
Secondary Accession Numbers
  • HMDB00525
Metabolite Identification
Common Name5-Hydroxyhexanoic acid
Description5-Hydroxyhexanoic acid is a normal dicarboxylic acid degradation product of fatty acids; however, it has been found in patients with non-ketotic dicarboxylic aciduria and one patient on a diet containing excessive amounts of medium-chain triglycerides. Increased amounts of dicarboxylic acids are excreted in human urine under conditions of medium-chain triglyceride (MCT) feeding, abnormal fatty acid oxidation (FAO) and fasting. Criteria to distinguish dicarboxylic aciduria originating from MCT feeding and other conditions are needed in urinary organic acid profiling for detecting inborn errors of metabolism. Medium-chain triglycerides (MCTs) are absorbed and metabolized differently from long-chain triglycerides (LCTs). MCTs may be useful as a dietary substitute in a variety of clinical disorders. Urinary excretion of 5-hydroxyhexanoic acid, the (omega-1) hydroxylation product, was increased during MCT feeding as compared with LCT feeding in patients with non-insulin-dependent diabetes mellitus (PMID: 6897376 , 2239769 , 8596483 ). Moreover, 5-hydroxyhexanoic acid is also found to be associated with Medium chain acyl-CoA dehydrogenase deficiency (MCADD), which is also an inborn error of metabolism. 5-Hydroxyhexanoic acid has be found to be a microbial metabolite (PMID: 20615997 ).
Structure
Data?1582752137
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000525 (5-Hydroxyhexanoic acid)

  Mrv0541 02231218342D          

  9  8  0  0  0  0            999 V2000
   14.2477   -8.3387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608   -8.3387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753   -9.5763    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187   -8.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898   -8.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333   -9.5763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  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
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000525 (5-Hydroxyhexanoic acid)

HMDB0000525
     RDKit          3D
5-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.7426    0.1163   -0.5853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7036   -0.1435    0.4592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5805   -1.5207    0.6204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    0.4825    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5994    0.1625    1.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9787    0.6986    1.0082 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6152    0.1633   -0.2424 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3366    0.7106   -1.3315 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4925   -0.9121   -0.2007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6103    0.6696   -0.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1888   -0.8379   -0.9792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3389    0.6288   -1.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2437    1.4697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8249   -1.9429   -0.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0476   -0.0175   -0.8497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4625    1.5592   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6812   -0.9485    1.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276    0.5431    2.1747 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6464    0.3766    1.8335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0223    1.8067    0.9992 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2781   -1.8387   -0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  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
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for HMDB0000525 (5-Hydroxyhexanoic acid)

  Mrv0541 02231218342D          

  9  8  0  0  0  0            999 V2000
   14.2477   -8.3387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9608   -8.3387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753   -9.5763    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8187   -8.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1043   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3898   -8.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5333   -9.5763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6753   -8.7512    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  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
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000525

> <DATABASE_NAME>
hmdb

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

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

> <INCHI_KEY>
YDCRNMJQROAWFT-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
14.061584100033663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxyhexanoic acid

> <ALOGPS_LOGP>
0.32

> <JCHEM_LOGP>
0.3462238706666664

> <ALOGPS_LOGS>
-0.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.759010245549824

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.710081342883259

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5920091843543904

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.8201

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000525 (5-Hydroxyhexanoic acid)

HMDB0000525
     RDKit          3D
5-Hydroxyhexanoic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.7426    0.1163   -0.5853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7036   -0.1435    0.4592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5805   -1.5207    0.6204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3483    0.4825    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5994    0.1625    1.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9787    0.6986    1.0082 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6152    0.1633   -0.2424 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3366    0.7106   -1.3315 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4925   -0.9121   -0.2007 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6103    0.6696   -0.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1888   -0.8379   -0.9792 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3389    0.6288   -1.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0301    0.2437    1.4697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8249   -1.9429   -0.2308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0476   -0.0175   -0.8497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4625    1.5592   -0.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6812   -0.9485    1.2699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2276    0.5431    2.1747 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6464    0.3766    1.8335 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0223    1.8067    0.9992 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2781   -1.8387   -0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  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
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for HMDB0000525 (5-Hydroxyhexanoic 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      26.596 -15.566   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      18.593 -15.566   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      19.927 -17.876   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      23.928 -15.566   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.595 -16.336   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.262 -16.336   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.261 -15.566   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.262 -17.876   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      19.927 -16.336   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    5    6                                                       
CONECT    5    4    7                                                       
CONECT    6    1    4    8                                                  
CONECT    7    5    9                                                       
CONECT    8    6                                                            
CONECT    9    2    3    7                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0000525 (5-Hydroxyhexanoic acid)

COMPND    HMDB0000525
HETATM    1  C1  UNL     1      -2.743   0.116  -0.585  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.704  -0.143   0.459  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.580  -1.521   0.620  1.00  0.00           O  
HETATM    4  C3  UNL     1      -0.348   0.482   0.098  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.599   0.163   1.201  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.979   0.699   1.008  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.615   0.163  -0.242  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.337   0.711  -1.331  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.492  -0.912  -0.201  1.00  0.00           O  
HETATM   10  H1  UNL     1      -3.610   0.670  -0.143  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.189  -0.838  -0.979  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.339   0.629  -1.480  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.030   0.244   1.470  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.825  -1.943  -0.231  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.048  -0.017  -0.850  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.463   1.559  -0.105  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.681  -0.948   1.270  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.228   0.543   2.175  1.00  0.00           H  
HETATM   19  H10 UNL     1       2.646   0.377   1.833  1.00  0.00           H  
HETATM   20  H11 UNL     1       2.022   1.807   0.999  1.00  0.00           H  
HETATM   21  H12 UNL     1       3.278  -1.839  -0.502  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4   13
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for HMDB0000525 (5-Hydroxyhexanoic acid)

CC(O)CCCC(O)=O
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INCHI for HMDB0000525 (5-Hydroxyhexanoic acid)

InChI=1S/C6H12O3/c1-5(7)3-2-4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Hydroxy caproic acidChEBI
5-Hydroxy-hexanoic acidChEBI
5-Hydroxycaproic acidChEBI
5-OH-Caproic acidChEBI
5-Hydroxy caproateGenerator
5-Hydroxy-hexanoateGenerator
5-HydroxycaproateGenerator
5-OH-CaproateGenerator
5-HydroxyhexanoateGenerator
5-Hydroxyhexanoic acidMeSH
Chemical FormulaC6H12O3
Average Molecular Weight132.1577
Monoisotopic Molecular Weight132.07864425
IUPAC Name5-hydroxyhexanoic acid
Traditional Name5-hydroxyhexanoic acid
CAS Registry Number44843-89-2
SMILES
CC(O)CCCC(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-5(7)3-2-4-6(8)9/h5,7H,2-4H2,1H3,(H,8,9)
InChI KeyYDCRNMJQROAWFT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Hydroxy fatty acid
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • 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 Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg125.79630932474
[M-H]-Not Available125.796http://allccs.zhulab.cn/database/detail?ID=AllCCS00000198
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
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. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. 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 ]
Medium Chain Acyl-CoA Dehydrogenase Deficiency
  1. Gregersen N, Kolvraa S, Rasmussen K, Mortensen PB, Divry P, David M, Hobolth N: General (medium-chain) acyl-CoA dehydrogenase deficiency (non-ketotic dicarboxylic aciduria): quantitative urinary excretion pattern of 23 biologically significant organic acids in three cases. Clin Chim Acta. 1983 Aug 15;132(2):181-91. [PubMed:6616873 ]
  2. Duran M, De Klerk JB, Wadman SK, Bruinvis L, Ketting D: The differential diagnosis of dicarboxylic aciduria. J Inherit Metab Dis. 1984;7 Suppl 1:48-51. [PubMed:6434845 ]
  3. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Associated OMIM IDs
  • 114500 (Colorectal cancer)
  • 201450 (Medium Chain Acyl-CoA Dehydrogenase Deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022093
KNApSAcK IDC00052163
Chemspider ID149280
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5510
PubChem Compound170748
PDB IDNot Available
ChEBI ID131434
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00029984
Good Scents IDNot Available
References
Synthesis ReferenceValentin, H. E.; Schoenebaum, A.; Steinbuechel, A. Identification of 5-hydroxyhexanoic acid, 4-hydroxyheptanoic acid and 4-hydroxyoctanoic acid as new constituents of bacterial polyhydroxyalkanoic acids. Applied Microbiology and Biotechnology (1996), 46(3), 261-267.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Boulat O, Gradwohl M, Matos V, Guignard JP, Bachmann C: Organic acids in the second morning urine in a healthy Swiss paediatric population. Clin Chem Lab Med. 2003 Dec;41(12):1642-58. [PubMed:14708889 ]
  2. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
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