Showing NP-Card for 5-hydroxyvaleric acid (NP0213041)

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Record Information
Version2.0
Created at2022-09-05 11:53:42 UTC
Updated at2022-09-05 11:53:42 UTC
NP-MRD IDNP0213041
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-hydroxyvaleric acid
Description5-Hydroxypentanoic acid, also known as 5-hydroxyvaleric acid or 4-oxy-butan-carbonsaeure, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 5-hydroxyvaleric acid is found in Trypanosoma brucei. 5-hydroxyvaleric acid was first documented in 1976 (PMID: 788806). 5-Hydroxypentanoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 1352515) (PMID: 1970730) (PMID: 2190964).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0213041 (5-hydroxyvaleric acid)

  Mrv0541 02231217542D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for NP0213041 (5-hydroxyvaleric acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
    2.4452   -1.4504   -0.6823 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2870   -0.5971    0.2262 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2229   -0.4360    1.2186 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0605    0.2336    0.1989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1958   -0.1298   -0.9804 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0563    0.6688   -1.0686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9501    0.5178    0.1379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3453   -0.8138    0.3229 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3931   -1.1438    1.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2974    1.2982    0.2515 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4718   -0.0648    1.1156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0211   -1.2002   -0.9921 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7971    0.0856   -1.8935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8299    1.7559   -1.1601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5996    0.3534   -1.9832 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8790    1.1017   -0.0610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3893    0.8815    1.0120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1003   -1.0604   -0.2533 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8 18  1  0
  7 16  1  0
  7 17  1  0
  6 14  1  0
  6 15  1  0
  5 12  1  0
  5 13  1  0
  4 10  1  0
  4 11  1  0
  3  9  1  0
M  END
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3D SDF for NP0213041 (5-hydroxyvaleric acid)

  Mrv0541 02231217542D          

  8  7  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0213041

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c6-4-2-1-3-5(7)8/h6H,1-4H2,(H,7,8)

> <INCHI_KEY>
PHOJOSOUIAQEDH-UHFFFAOYSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
12.181396826694243

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxypentanoic acid

> <ALOGPS_LOGP>
-0.23

> <JCHEM_LOGP>
-0.07035115399999997

> <ALOGPS_LOGS>
0.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
16.91852576987235

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.594243850553478

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9596369806312381

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
28.4013

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.43e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxyvaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0213041 (5-hydroxyvaleric acid)

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PDB for NP0213041 (5-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       3.286   3.437   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0213041 (5-hydroxyvaleric acid)
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SMILES for NP0213041 (5-hydroxyvaleric acid)
OCCCCC(O)=O
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INCHI for NP0213041 (5-hydroxyvaleric acid)
InChI=1S/C5H10O3/c6-4-2-1-3-5(7)8/h6H,1-4H2,(H,7,8)
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Synonyms
Chemical FormulaC5H10O3
Average Mass118.1311 Da
Monoisotopic Mass118.06299 Da
IUPAC Name5-hydroxypentanoic acid
Traditional Name5-hydroxyvaleric acid
CAS Registry NumberNot Available
SMILES
OCCCCC(O)=O
InChI Identifier
InChI=1S/C5H10O3/c6-4-2-1-3-5(7)8/h6H,1-4H2,(H,7,8)
InChI KeyPHOJOSOUIAQEDH-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Trypanosoma bruceiLOTUS Database
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
  • Hydroxy fatty acid
    • 

  • Straight chain fatty acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • 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
logP-0.23ALOGPS
logP-0.07ChemAxon
logS0.31ALOGPS
pKa (Strongest Acidic)4.59ChemAxon
pKa (Strongest Basic)-2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity28.4 m³·mol⁻¹ChemAxon
Polarizability12.18 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0061927  
DrugBank IDDB04781  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC02804  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Hydroxypentanoic acid  
METLIN IDNot Available
PubChem Compound25945  
PDB IDNot Available
ChEBI ID45564  
Good Scents IDNot Available
References
General References
  1. Matsumoto I, Kuhara T, Yoshino M: Metabolism of branched medium chain length fatty acid. II--beta-oxidation of sodium dipropylacetate in rats. Biomed Mass Spectrom. 1976 Oct;3(5):235-40. doi: 10.1002/bms.1200030509. [PubMed:788806  ] 
  2. Yamaki H, Yamaguchi M, Tsuruo T, Yamaguchi H: Mechanism of action of an antifungal antibiotic, RI-331, (S) 2-amino-4-oxo-5-hydroxypentanoic acid; kinetics of inactivation of homoserine dehydrogenase from Saccharomyces cerevisiae. J Antibiot (Tokyo). 1992 May;45(5):750-5. doi: 10.7164/antibiotics.45.750. [PubMed:1352515  ] 
  3. Yamaki H, Yamaguchi M, Imamura H, Suzuki H, Nishimura T, Saito H, Yamaguchi H: The mechanism of antifungal action of (S)-2-amino-4-oxo-5-hydroxypentanoic acid, RI-331: the inhibition of homoserine dehydrogenase in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 1990 Apr 30;168(2):837-43. doi:  10.1016/0006-291x(90)92397-i. [PubMed:1970730  ] 
  4. Yamaguchi M, Yamaki H, Shinoda T, Tago Y, Suzuki H, Nishimura T, Yamaguchi H: The mode of antifungal action of (S)2-amino-4-oxo-5-hydroxypentanoic acid, RI-331. J Antibiot (Tokyo). 1990 Apr;43(4):411-6. doi: 10.7164/antibiotics.43.411. [PubMed:2190964  ] 
  5. LOTUS database [Link]