Showing NP-Card for Valeric acid (NP0000153)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:40:02 UTC
NP-MRD IDNP0000153
Secondary Accession NumbersNone
Natural Product Identification
Common NameValeric acid
DescriptionValeric acid, or pentanoic acid, is a straight chain alkyl carboxylic acid with the chemical formula CH3(CH2)3COOH. Like other low molecular weight carboxylic acids, it has a very unpleasant odor. Valeric acid is commonly found in human feces, with an average concentration of 2.4 Umol/g feces (range of 0.6-3.8 Umol/g) (PMID: 6740214 ). Valeric acid is produced by the gut microbiota, typically Clostridia species and other gut bacterial species such as Megasphaera massiliensis MRx0029 (PMID: 30052654 ) Via the condensation of ethanol with propionic acid (PMID: 18116989 ). Valeric acid is largely considered as a gut microbial metabolite. Recently, valeric acid has been found to exert strong gut protective effects. Studies involving mice that received high doses of radiation showed that valeric acid replenishment (via oral gavage) elevated the survival rate of irradiated mice, protected hematogenic organs (such as the thymus and spleen), improved gastrointestinal (GI) tract function and enhanced intestinal epithelial integrity (PMID: 31931652 ). Valeric acid was also found to restore the enteric bacteria taxonomic proportions and reprogram the small intestinal protein profile to normal levels. Valeric acid, like butyric acid, also appears to be a potent histone deacetylase (HDAC) inhibitor. High levels of HDAC proteins have been implicated in a variety of disease pathologies, from cancer and colitis to cardiovascular disease and neurodegeneration (PMID: 30052654 ). Valeric acid is also found in certain plants, specifically in the perennial flowering plant valerian (Valeriana officinalis), from which it gets its name. Industrially valeric acid is primarily used is in the synthesis of its esters. Volatile esters of valeric acid tend to have pleasant odors and are used in perfumes and cosmetics. Ethyl valerate and pentyl valerate are used as food additives because of their fruity flavours. Hydrolysis of these valerate-containing food additives in the gut can also lead to the appearance of valerate in blood, urine and stool samples.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000153 (Valeric acid)

  Mrv1652305271900322D          

  7  6  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  5  7  2  0  0  0  0
M  END
Download

3D MOL for NP0000153 (Valeric acid)

HMDB0000892
     RDKit          3D
Valeric acid
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.3137    0.7689    0.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9656    0.1042    0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.0787   -0.8125 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1083   -0.7377   -0.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532    0.1223    0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6052    1.2796    0.5953 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1723   -0.3355    0.7784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8308    0.7310    1.2257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9479    0.2327   -0.4704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2320    1.8135   -0.0664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2170   -0.9343    0.8314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4263    0.6877    1.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8216   -0.6655   -1.5623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0464    0.9206   -1.2840 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6474   -0.9937   -1.4935 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891   -1.6618    0.0425 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5433   -1.2533    0.5814 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
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
M  END
Download

3D SDF for NP0000153 (Valeric acid)

  Mrv1652305271900322D          

  7  6  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    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
  5  7  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0000153

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)

> <INCHI_KEY>
NQPDZGIKBAWPEJ-UHFFFAOYSA-N

> <FORMULA>
C5H10O2

> <MOLECULAR_WEIGHT>
102.1317

> <EXACT_MASS>
102.068079564

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
11.225059262005129

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentanoic acid

> <ALOGPS_LOGP>
1.34

> <JCHEM_LOGP>
1.3663274626666666

> <ALOGPS_LOGS>
-0.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.013807378650193

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
26.4726

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-valeric acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0000153 (Valeric acid)

HMDB0000892
     RDKit          3D
Valeric acid
 17 16  0  0  0  0  0  0  0  0999 V2000
   -2.3137    0.7689    0.2420 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9656    0.1042    0.4624 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2105   -0.0787   -0.8125 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1083   -0.7377   -0.5499 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532    0.1223    0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6052    1.2796    0.5953 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1723   -0.3355    0.7784 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8308    0.7310    1.2257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9479    0.2327   -0.4704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2320    1.8135   -0.0664 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2170   -0.9343    0.8314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4263    0.6877    1.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8216   -0.6655   -1.5623 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0464    0.9206   -1.2840 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6474   -0.9937   -1.4935 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891   -1.6618    0.0425 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5433   -1.2533    0.5814 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
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
M  END
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PDB for NP0000153 (Valeric acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.977  -0.206   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    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0000153 (Valeric acid)

COMPND    HMDB0000892
HETATM    1  C1  UNL     1      -2.314   0.769   0.242  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.966   0.104   0.462  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.210  -0.079  -0.812  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.108  -0.738  -0.550  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.953   0.122   0.292  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.605   1.280   0.595  1.00  0.00           O  
HETATM    7  O2  UNL     1       3.172  -0.335   0.778  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.831   0.731   1.226  1.00  0.00           H  
HETATM    9  H2  UNL     1      -2.948   0.233  -0.470  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.232   1.814  -0.066  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.217  -0.934   0.831  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.426   0.688   1.188  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.822  -0.665  -1.562  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.046   0.921  -1.284  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.647  -0.994  -1.494  1.00  0.00           H  
HETATM   16  H9  UNL     1       0.889  -1.662   0.042  1.00  0.00           H  
HETATM   17  H10 UNL     1       3.543  -1.253   0.581  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6    6    7
CONECT    7   17
END
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SMILES for NP0000153 (Valeric acid)

CCCCC(O)=O
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INCHI for NP0000153 (Valeric acid)

InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)
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Synonyms
Chemical FormulaC5H10O2
Average Mass102.1317 Da
Monoisotopic Mass102.06808 Da
IUPAC Namepentanoic acid
Traditional NameN-valeric acid
CAS Registry Number109-52-4
SMILES
CCCCC(O)=O
InChI Identifier
InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)
InChI KeyNQPDZGIKBAWPEJ-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Chemical Taxonomy
Description Belongs to the class of organic compounds known as straight chain fatty acids. These are fatty acids with a straight aliphatic chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentStraight chain fatty acids
Alternative Parents
Substituents
  • Straight chain fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Experimental Properties
PropertyValueReference
Melting Point-34 °CNot Available
Boiling Point184.00 to 186.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility24 mg/mLNot Available
LogP1.39Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility40.3 g/LALOGPS
logP1.34ALOGPS
logP1.37ChemAxon
logS-0.4ALOGPS
pKa (Strongest Acidic)5.01ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity26.47 m³·mol⁻¹ChemAxon
Polarizability11.23 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000892
DrugBank IDDB02406
Phenol Explorer Compound IDNot Available
FoodDB IDFDB018739
KNApSAcK IDC00001208
Chemspider ID7701
KEGG Compound IDC00803
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkValeric acid
METLIN ID110
PubChem Compound7991
PDB IDNot Available
ChEBI ID17418
Good Scents IDrw1009341
References
General References