Showing NP-Card for 5-Hydroxyhexanoic acid (NP0136915)

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Record Information
Version2.0
Created at2022-05-12 17:05:48 UTC
Updated at2022-05-12 17:17:55 UTC
NP-MRD IDNP0136915
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-Hydroxyhexanoic acid
Description5-Hydroxyhexanoic acid, also known as 5-hydroxycaproate or 5-OH-caproic acid, 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. 5-Hydroxyhexanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 5-Hydroxyhexanoic acid was first documented in 1978 (PMID: 640132). 5-Hydroxyhexanoic acid, with regard to humans, has been found to be associated with the diseases such as colorectal cancer; 5-hydroxyhexanoic acid has also been linked to the inborn metabolic disorder medium chain acyl-coa dehydrogenase deficiency (PMID: 6897376) (PMID: 575058) (PMID: 6795215) (PMID: 8406236) (PMID: 2239769).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0136915 (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
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3D MOL for NP0136915 (5-Hydroxyhexanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.9697    0.5886    0.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8041   -0.2825   -0.2038 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8844   -0.6494   -1.5478 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5425    0.4830    0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7045   -0.3042   -0.2774 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8882    0.5815    0.0803 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1498   -0.1266   -0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2575    0.4196   -0.0513 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1062   -1.4026   -0.8202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6143    0.8688   -0.6481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5546    0.0622    1.0091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6415    1.5429    0.6722 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7963   -1.2331    0.3815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1813   -1.5909   -1.6528 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5450    0.7230    1.1715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5937    1.4452   -0.4526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6571   -0.4662   -1.3667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6869   -1.2221    0.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8276    1.5561   -0.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9148    0.8085    1.1608 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9349   -1.8017   -1.2273 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  9  1  0
  7  8  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  1
  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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3D SDF for NP0136915 (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>
NP0136915

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0136915 (5-Hydroxyhexanoic acid)

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PDB for NP0136915 (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 NP0136915 (5-Hydroxyhexanoic acid)
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SMILES for NP0136915 (5-Hydroxyhexanoic acid)
CC(O)CCCC(O)=O
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INCHI for NP0136915 (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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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 Mass132.1577 Da
Monoisotopic Mass132.07864 Da
IUPAC Name5-hydroxyhexanoic acid
Traditional Name5-hydroxyhexanoic acid
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.32ALOGPS
logP0.35ChemAxon
logS-0.02ALOGPS
pKa (Strongest Acidic)4.71ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.82 m³·mol⁻¹ChemAxon
Polarizability14.06 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000525  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022093  
KNApSAcK IDNot Available
Chemspider ID149280  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5510  
PubChem Compound170748  
PDB IDNot Available
ChEBI ID131434  
Good Scents IDNot Available
References
General References
  1. Kamerling JP, Duran M, Bruinvis L, Ketting D, Wadman SK, Vliegenthart JF: The absolute configuration of urinary 5-hydroxyhexanoic acid - a product of fatty acid (omega-1)-oxidation - in patients with non-ketotic dicarboxylic aciduria. Clin Chim Acta. 1982 Nov 10;125(3):247-54. doi: 10.1016/0009-8981(82)90254-6. [PubMed:6897376  ] 
  2. Chalmers RA, Lawson AM: Identification of 5-hydroxyhexanoic acid in the urine of twin siblings with a Reye's-like syndrome associated with dicarboxylic aciduria and hypoglycaemia and with similarities to Jamaican vomiting sickness. Biomed Mass Spectrom. 1979 Oct;6(10):444-6. doi: 10.1002/bms.1200061008. [PubMed:575058  ] 
  3. Lawson AM, Chalmers RA: Identification of 5-hydroxyhexanoic acid in the urine of twin siblings with a syndrome having close similarities to Jamaican vomiting sickness [proceedings]. Biochem Soc Trans. 1978;6(1):108-10. doi: 10.1042/bst0060108. [PubMed:640132  ] 
  4. Niwa T, Meada K, Ohki T, Saito A, Tsuchida I: Gas chromatographic-mass spectrometric profile of organic acids in urine and serum of diabetic ketotic patients. J Chromatogr. 1981 Sep 11;225(1):1-8. doi: 10.1016/s0378-4347(00)80237-6. [PubMed:6795215  ] 
  5. Loftus NJ, Laird WJ, Steel GT, Wilks MF, Woollen BH: Metabolism and pharmacokinetics of deuterium-labelled di-2-(ethylhexyl) adipate (DEHA) in humans. Food Chem Toxicol. 1993 Sep;31(9):609-14. doi: 10.1016/0278-6915(93)90042-w. [PubMed:8406236  ] 
  6. Brass EP, Tserng KY, Eckel RH: Urinary organic acid excretion during feeding of medium-chain or long-chain triglyceride diets in patients with non-insulin-dependent diabetes mellitus. Am J Clin Nutr. 1990 Nov;52(5):923-6. doi: 10.1093/ajcn/52.5.923. [PubMed:2239769  ]