Showing NP-Card for Benzoic acid (NP0001345)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Show more...Show more...Show more...Show more...
Record Information
Version2.0
Created at2006-02-23 11:42:39 UTC
Updated at2024-09-03 04:21:26 UTC
NP-MRD IDNP0001345
Natural Product DOIhttps://doi.org/10.57994/2485
Secondary Accession NumbersNone
Natural Product Identification
Common NameBenzoic acid
DescriptionBenzoic acid, C6H5COOH, is a colourless crystalline solid and the simplest aromatic carboxylic acid. Benzoic acid occurs naturally free and bound as benzoic acid esters in many plant and animal species. Appreciable amounts have been found in most berries (around 0.05%). Cranberries contain as much as 300-1300 mg free benzoic acid per kg fruit. Benzoic acid is a fungistatic compound that is widely used as a food preservative. It often is conjugated to glycine in the liver and excreted as hippuric acid. Benzoic acid is a byproduct of phenylalanine metabolism in bacteria. It is also produced when gut bacteria process polyphenols (from ingested fruits or beverages). It can be found in Serratia (PMID: 23061754 ).
Structure
Data?1628564085
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0001345 (Benzoic acid)

  Mrv1652306242117433D          

 15 15  0  0  0  0            999 V2000
   -2.4090   -1.7052    0.4637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0548   -0.5378    0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9747    0.4469    0.0288 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6353   -0.2421    0.1183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1732    1.0434   -0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1778    1.2917   -0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1272    0.3089   -0.0601 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6803   -0.9560    0.2135 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327   -1.2170    0.2989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2572    0.8533   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9032    1.8127   -0.3032 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5263    2.3123   -0.4632 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1803    0.5634   -0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4160   -1.7563    0.3631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0333   -2.2181    0.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9  4  1  0  0  0  0
  3 10  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
  7 13  1  0  0  0  0
  8 14  1  0  0  0  0
  9 15  1  0  0  0  0
M  END
Download

3D MOL for NP0001345 (Benzoic acid)

HMDB0001870
     RDKit          3D
Benzoic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.8504   -0.0733    1.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9303   -0.7764    0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1383   -2.1199    0.2496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6310   -0.1958    0.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4238    1.1175    0.6788 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8226    1.7060    0.4766 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8554    0.9527   -0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6590   -0.3791   -0.3818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3938   -0.9411   -0.1662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0810   -2.2945   -0.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1929    1.7615    1.0971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9675    2.7358    0.7332 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8009    1.4473   -0.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4721   -0.9586   -0.7945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2765   -1.9822   -0.4344 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  3 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
  8 14  1  0
  9 15  1  0
M  END
Download

3D SDF for NP0001345 (Benzoic acid)

  Mrv1652306242117433D          

 15 15  0  0  0  0            999 V2000
   -2.4090   -1.7052    0.4637 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0548   -0.5378    0.2126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9747    0.4469    0.0288 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6353   -0.2421    0.1183 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1732    1.0434   -0.1599 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1778    1.2917   -0.2428 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1272    0.3089   -0.0601 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6803   -0.9560    0.2135 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327   -1.2170    0.2989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2572    0.8533   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9032    1.8127   -0.3032 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5263    2.3123   -0.4632 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1803    0.5634   -0.1373 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4160   -1.7563    0.3631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0333   -2.2181    0.5157 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9  4  1  0  0  0  0
  3 10  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
  7 13  1  0  0  0  0
  8 14  1  0  0  0  0
  9 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0001345

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C1=C([H])C([H])=C([H])C([H])=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)

> <INCHI_KEY>
WPYMKLBDIGXBTP-UHFFFAOYSA-N

> <FORMULA>
C7H6O2

> <MOLECULAR_WEIGHT>
122.123

> <EXACT_MASS>
122.036779433

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.97308273996681

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
benzoic acid

> <ALOGPS_LOGP>
1.72

> <JCHEM_LOGP>
1.630828724

> <ALOGPS_LOGS>
-1.24

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.07523327743486

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
33.3142

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.08e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
benzoic acid

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0001345 (Benzoic acid)

HMDB0001870
     RDKit          3D
Benzoic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
   -2.8504   -0.0733    1.0595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9303   -0.7764    0.5787 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1383   -2.1199    0.2496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6310   -0.1958    0.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4238    1.1175    0.6788 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8226    1.7060    0.4766 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8554    0.9527   -0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6590   -0.3791   -0.3818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3938   -0.9411   -0.1662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0810   -2.2945   -0.7659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1929    1.7615    1.0971 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9675    2.7358    0.7332 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8009    1.4473   -0.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4721   -0.9586   -0.7945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2765   -1.9822   -0.4344 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9  4  1  0
  3 10  1  0
  5 11  1  0
  6 12  1  0
  7 13  1  0
  8 14  1  0
  9 15  1  0
M  END
Download

PDB for NP0001345 (Benzoic acid)

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0      -2.409  -1.705   0.464  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.055  -0.538   0.213  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.975   0.447   0.029  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.635  -0.242   0.118  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.173   1.043  -0.160  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.178   1.292  -0.243  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.127   0.309  -0.060  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.680  -0.956   0.214  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.333  -1.217   0.299  0.00  0.00           C+0
HETATM   10  H   UNK     0      -3.257   0.853  -0.848  0.00  0.00           H+0
HETATM   11  H   UNK     0      -0.903   1.813  -0.303  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.526   2.312  -0.463  0.00  0.00           H+0
HETATM   13  H   UNK     0       3.180   0.563  -0.137  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.416  -1.756   0.363  0.00  0.00           H+0
HETATM   15  H   UNK     0      -0.033  -2.218   0.516  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   10                                                       
CONECT    4    2    5    9                                                  
CONECT    5    4    6   11                                                  
CONECT    6    5    7   12                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7    9   14                                                  
CONECT    9    8    4   15                                                  
CONECT   10    3                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END
Download

3D PDB for NP0001345 (Benzoic acid)

COMPND    HMDB0001870
HETATM    1  O1  UNL     1      -2.850  -0.073   1.059  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.930  -0.776   0.579  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.138  -2.120   0.250  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.631  -0.196   0.358  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.424   1.118   0.679  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.823   1.706   0.477  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.855   0.953  -0.053  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.659  -0.379  -0.382  1.00  0.00           C  
HETATM    9  C7  UNL     1       0.394  -0.941  -0.166  1.00  0.00           C  
HETATM   10  H1  UNL     1      -2.081  -2.294  -0.766  1.00  0.00           H  
HETATM   11  H2  UNL     1      -1.193   1.762   1.097  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.967   2.736   0.733  1.00  0.00           H  
HETATM   13  H4  UNL     1       2.801   1.447  -0.192  1.00  0.00           H  
HETATM   14  H5  UNL     1       2.472  -0.959  -0.794  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.276  -1.982  -0.434  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    5    9
CONECT    5    6   11
CONECT    6    7    7   12
CONECT    7    8   13
CONECT    8    9    9   14
CONECT    9   15
END
Download

SMILES for NP0001345 (Benzoic acid)

[H]OC(=O)C1=C([H])C([H])=C([H])C([H])=C1[H]
Download

INCHI for NP0001345 (Benzoic acid)

InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)
Download
View in JSmol
Synonyms
Chemical FormulaC7H6O2
Average Mass122.1230 Da
Monoisotopic Mass122.03678 Da
IUPAC Namebenzoic acid
Traditional Namebenzoic acid
CAS Registry Number65-85-0
SMILES
[H]OC(=O)C1=C([H])C([H])=C([H])C([H])=C1[H]
InChI Identifier
InChI=1S/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)
InChI KeyWPYMKLBDIGXBTP-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, simulated)Ahselim2022-01-11View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)hxkuang@hljucm.netNot AvailableNot Available2024-05-11View Spectrum
1D NMR1H NMR Spectrum (1D, 600 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
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, simulated)Not AvailableNot AvailableNot Available2024-05-11View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Homo sapiens (Exhaled breath)KNApSAcK Database
Homo sapiens (Feces)KNApSAcK Database
Phoma medicaginisKNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzoic acids. These are organic Compounds containing a benzene ring which bears at least one carboxyl group.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzoic acids and derivatives
Direct ParentBenzoic acids
Alternative Parents
Substituents
  • Benzoic acid
  • Benzoyl
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point122.4 °CNot Available
Boiling Point132.00 to 133.00 °C. @ 10.00 mm HgThe Good Scents Company Information System
Water Solubility3.4 mg/mL at 25 °CNot Available
LogP1.87Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility7.08 g/LALOGPS
logP1.72ALOGPS
logP1.63ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)4.08ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.31 m³·mol⁻¹ChemAxon
Polarizability11.97 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001870
DrugBank IDDB03793
Phenol Explorer Compound ID427
FoodDB IDFDB008739
KNApSAcK IDC00000207
Chemspider ID238
KEGG Compound IDC00539
BioCyc IDBENZOATE
BiGG ID34156
Wikipedia LinkBenzoic_Acid
METLIN ID1297
PubChem Compound243
PDB IDNot Available
ChEBI ID30746
Good Scents IDrw1033731
References
General References