Showing metabocard for Valeric acid (MMDBc0000165)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:38:15 UTC
Update Date2024-09-28 01:29:00 UTC
Metabolite IDMMDBc0000165
Metabolite 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 a 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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f923a168ef0>


  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
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3D MOL for #<Metabolite:0x00007f923a168ef0>

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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3D SDF for #<Metabolite:0x00007f923a168ef0>


  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>
MMDBc0000165

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f923a168ef0>

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 #<Metabolite:0x00007f923a168ef0>

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 #<Metabolite:0x00007f923a168ef0>

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 #<Metabolite:0x00007f923a168ef0>

CCCCC(O)=O
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INCHI for #<Metabolite:0x00007f923a168ef0>

InChI=1S/C5H10O2/c1-2-3-4-5(6)7/h2-4H2,1H3,(H,6,7)
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Synonyms
ValueSource
1-Butanecarboxylic acidChEBI
CH3-[CH2]3-COOHChEBI
N-BuCOOHChEBI
N-PentanoateChEBI
N-Pentanoic acidChEBI
N-Valeric acidChEBI
PentanoateChEBI
Pentanoic acidChEBI
Pentoic acidChEBI
Propylacetic acidChEBI
ValerateChEBI
Valerianic acidChEBI
ValeriansaeureChEBI
Valeric acid, normalChEBI
1-ButanecarboxylateGenerator
N-ValerateGenerator
PentoateGenerator
PropylacetateGenerator
ValerianateGenerator
Valerate, normalGenerator
1-PentanoateHMDB
1-Pentanoic acidHMDB
ButanecarboxylateHMDB
Butanecarboxylic acidHMDB
Kyselina valerovaHMDB
N-C4H9COOHHMDB
ValeriansaureHMDB
Valeric acid normalHMDB
N-Pentanoic acid, ammonium saltHMDB
N-Pentanoic acid, potassium saltHMDB
N-Pentanoic acid, sodium saltHMDB
N-Pentanoic acid, zinc saltHMDB
N-Pentanoic acid, maganese (+2) saltHMDB
N-Pentanoic acid, 11C-labeledHMDB
Lithium pentanoateHMDB
N-Pentanoic acid, 11C-labeled sodium saltHMDB
Valeric acidKEGG
Molecular FormulaC5H10O2
Average Mass102.1317
Monoisotopic Mass102.068079564
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