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Showing metabocard for Benzocaine (HMDB0004992)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-10-16 10:59:41 UTC
Update Date2023-02-21 17:17:06 UTC
HMDB IDHMDB0004992
Secondary Accession Numbers
  • HMDB04992
Metabolite Identification
Common NameBenzocaine
DescriptionBenzocaine is a surface anesthetic that acts by preventing transmission of impulses along nerve fibers and at nerve endings. Benzocaine is a local anesthetic commonly used as a topical pain reliever. It is the active ingredient in many over-the-counter analgesic ointments. Benzocaine is an ester, a compound made from the organic acid PABA (para-aminobenzoic acid) and ethanol. The process in which this ester is created is known as Fischer esterification.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0004992 (Benzocaine)

1086
  Mrv1652305271900032D          

 12 12  0  0  0  0            999 V2000
    3.0791    1.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -2.3472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.1279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.5222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -1.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.9529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    2.6029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  2 10  2  0  0  0  0
  3  7  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  4 10  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
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3D MOL for HMDB0004992 (Benzocaine)

HMDB0004992
     RDKit          3D
Benzocaine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -3.8180    0.9016   -0.1749 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3666   -0.4917   -0.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -0.5075   -0.6980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1754   -0.1372    0.3824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6600    0.2058    1.4874 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2831   -0.1397    0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0815    0.2238    1.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4494    0.2263    1.1981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0665   -0.1341    0.0276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4849   -0.1303   -0.0825 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2606   -0.5005   -1.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8831   -0.5054   -0.9364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9780    0.9446    0.9251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7214    1.2171   -0.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0289    1.6602   -0.4337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5762   -1.2258    0.3022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9011   -0.8208   -1.4283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6397    0.5239    2.2767 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0272    0.5285    2.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9655    0.7491   -0.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0316   -0.9951    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7298   -0.7896   -1.9762 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2855   -0.8031   -1.8083 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  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12  6  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  7 18  1  0
  8 19  1  0
 10 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
M  END
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3D SDF for HMDB0004992 (Benzocaine)

1086
  Mrv1652305271900032D          

 12 12  0  0  0  0            999 V2000
    3.0791    1.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.3654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -2.3472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.1279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.2846    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645   -1.5222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791   -1.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.1096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3645    0.9529    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0791    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7935    2.6029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  2 10  2  0  0  0  0
  3  7  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  4 10  1  0  0  0  0
  5  8  1  0  0  0  0
  6  9  2  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
 11 12  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0004992

> <DATABASE_NAME>
hmdb

> <SMILES>
CCOC(=O)C1=CC=C(N)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3

> <INCHI_KEY>
BLFLLBZGZJTVJG-UHFFFAOYSA-N

> <FORMULA>
C9H11NO2

> <MOLECULAR_WEIGHT>
165.1891

> <EXACT_MASS>
165.078978601

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.458940489590255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
ethyl 4-aminobenzoate

> <ALOGPS_LOGP>
2.20

> <JCHEM_LOGP>
1.5046047806666665

> <ALOGPS_LOGS>
-1.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
2.7762371036930076

> <JCHEM_POLAR_SURFACE_AREA>
52.32

> <JCHEM_REFRACTIVITY>
47.532300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.85e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
benzocaine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0004992 (Benzocaine)

HMDB0004992
     RDKit          3D
Benzocaine
 23 23  0  0  0  0  0  0  0  0999 V2000
   -3.8180    0.9016   -0.1749 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3666   -0.4917   -0.5284 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9627   -0.5075   -0.6980 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1754   -0.1372    0.3824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6600    0.2058    1.4874 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2831   -0.1397    0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0815    0.2238    1.3080 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4494    0.2263    1.1981 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0665   -0.1341    0.0276 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4849   -0.1303   -0.0825 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2606   -0.5005   -1.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8831   -0.5054   -0.9364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9780    0.9446    0.9251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7214    1.2171   -0.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0289    1.6602   -0.4337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5762   -1.2258    0.3022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9011   -0.8208   -1.4283 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6397    0.5239    2.2767 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0272    0.5285    2.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9655    0.7491   -0.3585 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0316   -0.9951    0.1107 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7298   -0.7896   -1.9762 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2855   -0.8031   -1.8083 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  2  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  2  0
 12  6  1  0
  1 13  1  0
  1 14  1  0
  1 15  1  0
  2 16  1  0
  2 17  1  0
  7 18  1  0
  8 19  1  0
 10 20  1  0
 10 21  1  0
 11 22  1  0
 12 23  1  0
M  END
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PDB for HMDB0004992 (Benzocaine)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 1086                                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0       5.748   2.549   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       3.080   2.549   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0       4.414  -4.381   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       4.414   0.239   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.748  -0.531   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.080  -0.531   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.414  -2.841   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.748  -2.071   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.080  -2.071   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.414   1.779   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.748   4.089   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.081   4.859   0.000  0.00  0.00           C+0
CONECT    1   10   11                                                       
CONECT    2   10                                                            
CONECT    3    7                                                            
CONECT    4    5    6   10                                                  
CONECT    5    4    8                                                       
CONECT    6    4    9                                                       
CONECT    7    3    8    9                                                  
CONECT    8    5    7                                                       
CONECT    9    6    7                                                       
CONECT   10    1    2    4                                                  
CONECT   11    1   12                                                       
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0004992 (Benzocaine)

COMPND    HMDB0004992
HETATM    1  C1  UNL     1      -3.818   0.902  -0.175  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.367  -0.492  -0.528  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.963  -0.507  -0.698  1.00  0.00           O  
HETATM    4  C3  UNL     1      -1.175  -0.137   0.382  1.00  0.00           C  
HETATM    5  O2  UNL     1      -1.660   0.206   1.487  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.283  -0.140   0.249  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.081   0.224   1.308  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.449   0.226   1.198  1.00  0.00           C  
HETATM    9  C7  UNL     1       3.066  -0.134   0.028  1.00  0.00           C  
HETATM   10  N1  UNL     1       4.485  -0.130  -0.082  1.00  0.00           N  
HETATM   11  C8  UNL     1       2.261  -0.500  -1.039  1.00  0.00           C  
HETATM   12  C9  UNL     1       0.883  -0.505  -0.936  1.00  0.00           C  
HETATM   13  H1  UNL     1      -3.978   0.945   0.925  1.00  0.00           H  
HETATM   14  H2  UNL     1      -4.721   1.217  -0.742  1.00  0.00           H  
HETATM   15  H3  UNL     1      -3.029   1.660  -0.434  1.00  0.00           H  
HETATM   16  H4  UNL     1      -3.576  -1.226   0.302  1.00  0.00           H  
HETATM   17  H5  UNL     1      -3.901  -0.821  -1.428  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.640   0.524   2.277  1.00  0.00           H  
HETATM   19  H7  UNL     1       3.027   0.528   2.086  1.00  0.00           H  
HETATM   20  H8  UNL     1       4.965   0.749  -0.358  1.00  0.00           H  
HETATM   21  H9  UNL     1       5.032  -0.995   0.111  1.00  0.00           H  
HETATM   22  H10 UNL     1       2.730  -0.790  -1.976  1.00  0.00           H  
HETATM   23  H11 UNL     1       0.285  -0.803  -1.808  1.00  0.00           H  
CONECT    1    2   13   14   15
CONECT    2    3   16   17
CONECT    3    4
CONECT    4    5    5    6
CONECT    6    7    7   12
CONECT    7    8   18
CONECT    8    9    9   19
CONECT    9   10   11
CONECT   10   20   21
CONECT   11   12   12   22
CONECT   12   23
END
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SMILES for HMDB0004992 (Benzocaine)

CCOC(=O)C1=CC=C(N)C=C1
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INCHI for HMDB0004992 (Benzocaine)

InChI=1S/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC9H11NO2
Average Molecular Weight165.1891
Monoisotopic Molecular Weight165.078978601
IUPAC Nameethyl 4-aminobenzoate
Traditional Namebenzocaine
CAS Registry Number94-09-7
SMILES
CCOC(=O)C1=CC=C(N)C=C1
InChI Identifier
InChI=1S/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3
InChI KeyBLFLLBZGZJTVJG-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzoic acid esters. These are ester derivatives of benzoic acid.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzoic acids and derivatives
Direct ParentBenzoic acid esters
Alternative Parents
Substituents
  • Aminobenzoic acid or derivatives
  • Benzoate ester
  • Benzoyl
  • Aniline or substituted anilines
  • Amino acid or derivatives
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Amine
  • Organonitrogen compound
  • Organooxygen compound
  • Primary amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point92 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility23320 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.86HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+CBM148.230932474
[M+H]+Not Available145.903http://allccs.zhulab.cn/database/detail?ID=AllCCS00000755
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01086
Phenol Explorer Compound IDNot Available
FooDB IDFDB023574
KNApSAcK IDNot Available
Chemspider ID13854242
KEGG Compound IDC07527
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBenzocaine
METLIN ID3934
PubChem Compound2337
PDB IDNot Available
ChEBI ID116735
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1836611
References
Synthesis ReferenceSalts from naphtholmonosulphonic acids and p-aminobensoic acid ethyl ether. (1904), DE 181324 19040213 CAN 1:9748 AN 1907:9748
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Bong CL, Hilliard J, Seefelder C: Severe methemoglobinemia from topical benzocaine 7.5% (baby orajel) use for teething pain in a toddler. Clin Pediatr (Phila). 2009 Mar;48(2):209-11. doi: 10.1177/0009922808324491. Epub 2008 Oct 3. [PubMed:18836057 ]
  2. FENTON PF, COWGILL GR, STONE MA, JUSTICE DH: The nutrition of the mouse. VIII. Studies on pantothenic acid, biotin, inositol and paminobenzoic acid. J Nutr. 1950 Oct;42(2):257-69. [PubMed:14795275 ]

Enzymes

Enzyme Details
1. Sodium channel protein type 10 subunit alpha
General function:
Involved in ion channel activity
Specific function:
This protein mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which sodium ions may pass in accordance with their electrochemical gradient. It is a tetrodotoxin-resistant sodium channel isoform. Its electrophysiological properties vary depending on the type of the associated beta subunits (in vitro). Plays a role in neuropathic pain mechanisms
Gene Name:
SCN10A
Uniprot ID:
Q9Y5Y9
Molecular weight:
220623.6