Hmdb loader

Showing metabocard for Carbendazim (HMDB0031769)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:45:21 UTC
Update Date2023-02-21 17:21:18 UTC
HMDB IDHMDB0031769
Secondary Accession Numbers
  • HMDB31769
Metabolite Identification
Common NameCarbendazim
DescriptionCarbendazim, also known as bavistin or kolfugo, belongs to the class of organic compounds known as 2-benzimidazolylcarbamic acid esters. These are aromatic heteropolycyclic compounds that contain a carbamic acid ester group, which is N-linked to the C2-atom of a benzimidazole moiety. Carbendazim is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on Carbendazim.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031769 (Carbendazim)

  Mrv1652307282022152D          

 14 15  0  0  0  0            999 V2000
    1.0521   -0.3641    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666    0.2827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1617    0.0399    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1617   -0.7690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093   -1.3359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473   -2.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617   -2.3884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7287   -1.8215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666   -1.0117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8093    1.0117    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3238    1.6593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666    2.3884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4851    1.4973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0521    2.0642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  1  0  0  0  0
  2  3  2  0  0  0  0
  2 10  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  9  1  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
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031769 (Carbendazim)

HMDB0031769
     RDKit          3D
Carbendazim
 23 24  0  0  0  0  0  0  0  0999 V2000
    4.1395    1.1943    0.4023 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8921    0.5583    0.0850 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8807   -0.5758   -0.7149 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9827   -1.0028   -1.1331 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7009   -1.2684   -1.0794 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4113   -0.8058   -0.6163 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1674    0.2614    0.1634 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1682    0.3622    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9872    1.2246    1.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3679    1.0805    1.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9603    0.0319    0.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1487   -0.8373   -0.2621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7714   -0.6831   -0.2988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7618   -1.3601   -0.8838 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9965    1.6427    1.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3957    1.9634   -0.3649 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9586    0.4330    0.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7755   -2.1025   -1.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5539    2.0384    1.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9992    1.7797    1.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0374   -0.0575    0.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6272   -1.6525   -0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9177   -2.2248   -1.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14  6  1  0
 13  8  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  5 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
M  END
Download

3D SDF for HMDB0031769 (Carbendazim)

  Mrv1652307282022152D          

 14 15  0  0  0  0            999 V2000
    1.0521   -0.3641    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666    0.2827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1617    0.0399    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1617   -0.7690    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093   -1.3359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6473   -2.1457    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1617   -2.3884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7287   -1.8215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666   -1.0117    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8093    1.0117    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3238    1.6593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5666    2.3884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4851    1.4973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0521    2.0642    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  1  0  0  0  0
  2  3  2  0  0  0  0
  2 10  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  9  1  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
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031769

> <DATABASE_NAME>
hmdb

> <SMILES>
COC(=O)NC1=NC2=CC=CC=C2N1

> <INCHI_IDENTIFIER>
InChI=1S/C9H9N3O2/c1-14-9(13)12-8-10-6-4-2-3-5-7(6)11-8/h2-5H,1H3,(H2,10,11,12,13)

> <INCHI_KEY>
TWFZGCMQGLPBSX-UHFFFAOYSA-N

> <FORMULA>
C9H9N3O2

> <MOLECULAR_WEIGHT>
191.1867

> <EXACT_MASS>
191.069476547

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
19.46332015286911

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl N-(1H-1,3-benzodiazol-2-yl)carbamate

> <ALOGPS_LOGP>
1.46

> <JCHEM_LOGP>
1.8007555073333332

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.947962791374731

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.699461258315827

> <JCHEM_PKA_STRONGEST_BASIC>
4.277316683438969

> <JCHEM_POLAR_SURFACE_AREA>
67.01

> <JCHEM_REFRACTIVITY>
50.9284

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.25e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
carbendazim

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0031769 (Carbendazim)

HMDB0031769
     RDKit          3D
Carbendazim
 23 24  0  0  0  0  0  0  0  0999 V2000
    4.1395    1.1943    0.4023 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8921    0.5583    0.0850 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8807   -0.5758   -0.7149 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9827   -1.0028   -1.1331 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7009   -1.2684   -1.0794 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4113   -0.8058   -0.6163 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1674    0.2614    0.1634 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1682    0.3622    0.3758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9872    1.2246    1.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3679    1.0805    1.1158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9603    0.0319    0.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1487   -0.8373   -0.2621 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7714   -0.6831   -0.2988 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7618   -1.3601   -0.8838 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9965    1.6427    1.4088 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3957    1.9634   -0.3649 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9586    0.4330    0.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7755   -2.1025   -1.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5539    2.0384    1.6007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9992    1.7797    1.6765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0374   -0.0575    0.4885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6272   -1.6525   -0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9177   -2.2248   -1.4781 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14  6  1  0
 13  8  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  5 18  1  0
  9 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 14 23  1  0
M  END
Download

PDB for HMDB0031769 (Carbendazim)

HEADER    PROTEIN                                 28-JUL-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-JUL-20         0                                  
HETATM    1  N   UNK     0       1.964  -0.680   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.058   0.528   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.302   0.074   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -0.302  -1.435   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.511  -2.494   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.208  -4.005   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.302  -4.458   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.360  -3.400   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.058  -1.889   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.511   1.889   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       0.604   3.097   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       1.058   4.458   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.906   2.795   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.964   3.853   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3   10                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    1    4    8                                                  
CONECT   10    2   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END
Download

3D PDB for HMDB0031769 (Carbendazim)

COMPND    HMDB0031769
HETATM    1  C1  UNL     1       4.140   1.194   0.402  1.00  0.00           C  
HETATM    2  O1  UNL     1       2.892   0.558   0.085  1.00  0.00           O  
HETATM    3  C2  UNL     1       2.881  -0.576  -0.715  1.00  0.00           C  
HETATM    4  O2  UNL     1       3.983  -1.003  -1.133  1.00  0.00           O  
HETATM    5  N1  UNL     1       1.701  -1.268  -1.079  1.00  0.00           N  
HETATM    6  C3  UNL     1       0.411  -0.806  -0.616  1.00  0.00           C  
HETATM    7  N2  UNL     1       0.167   0.261   0.163  1.00  0.00           N  
HETATM    8  C4  UNL     1      -1.168   0.362   0.376  1.00  0.00           C  
HETATM    9  C5  UNL     1      -1.987   1.225   1.072  1.00  0.00           C  
HETATM   10  C6  UNL     1      -3.368   1.081   1.116  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.960   0.032   0.438  1.00  0.00           C  
HETATM   12  C8  UNL     1      -3.149  -0.837  -0.262  1.00  0.00           C  
HETATM   13  C9  UNL     1      -1.771  -0.683  -0.299  1.00  0.00           C  
HETATM   14  N3  UNL     1      -0.762  -1.360  -0.884  1.00  0.00           N  
HETATM   15  H1  UNL     1       3.997   1.643   1.409  1.00  0.00           H  
HETATM   16  H2  UNL     1       4.396   1.963  -0.365  1.00  0.00           H  
HETATM   17  H3  UNL     1       4.959   0.433   0.469  1.00  0.00           H  
HETATM   18  H4  UNL     1       1.776  -2.102  -1.677  1.00  0.00           H  
HETATM   19  H5  UNL     1      -1.554   2.038   1.601  1.00  0.00           H  
HETATM   20  H6  UNL     1      -3.999   1.780   1.676  1.00  0.00           H  
HETATM   21  H7  UNL     1      -5.037  -0.058   0.488  1.00  0.00           H  
HETATM   22  H8  UNL     1      -3.627  -1.653  -0.787  1.00  0.00           H  
HETATM   23  H9  UNL     1      -0.918  -2.225  -1.478  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3
CONECT    3    4    4    5
CONECT    5    6   18
CONECT    6    7    7   14
CONECT    7    8
CONECT    8    9    9   13
CONECT    9   10   19
CONECT   10   11   11   20
CONECT   11   12   21
CONECT   12   13   13   22
CONECT   13   14
CONECT   14   23
END
Download

SMILES for HMDB0031769 (Carbendazim)

COC(=O)NC1=NC2=CC=CC=C2N1
Download

INCHI for HMDB0031769 (Carbendazim)

InChI=1S/C9H9N3O2/c1-14-9(13)12-8-10-6-4-2-3-5-7(6)11-8/h2-5H,1H3,(H2,10,11,12,13)
Download
View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC9H9N3O2
Average Molecular Weight191.1867
Monoisotopic Molecular Weight191.069476547
IUPAC Namemethyl N-(1H-1,3-benzodiazol-2-yl)carbamate
Traditional Namecarbendazim
CAS Registry Number10605-21-7
SMILES
COC(=O)NC1=NC2=CC=CC=C2N1
InChI Identifier
InChI=1S/C9H9N3O2/c1-14-9(13)12-8-10-6-4-2-3-5-7(6)11-8/h2-5H,1H3,(H2,10,11,12,13)
InChI KeyTWFZGCMQGLPBSX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2-benzimidazolylcarbamic acid esters. These are aromatic heteropolycyclic compounds that contain a carbamic acid ester group, which is N-linked to the C2-atom of a benzimidazole moiety.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzimidazoles
Sub Class2-benzimidazolylcarbamic acid esters
Direct Parent2-benzimidazolylcarbamic acid esters
Alternative Parents
Substituents
  • 2-benzimidazolylcarbamic acid ester
  • Benzenoid
  • Azole
  • Imidazole
  • Carbamic acid ester
  • Heteroaromatic compound
  • Carbonic acid derivative
  • Azacycle
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationEnvironmental role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point302 - 307 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility29 mg/L @ 24C (exp)The Good Scents Company Information System
LogP1.52Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB13009
Phenol Explorer Compound IDNot Available
FooDB IDFDB008442
KNApSAcK IDNot Available
Chemspider ID23741
KEGG Compound IDC10897
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCarbendazim
METLIN IDNot Available
PubChem Compound25429
PDB IDNot Available
ChEBI ID3392
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1227191
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Narayana KJ, Prabhakar P, Vijayalakshmi M, Venkateswarlu Y, Krishna PS: Biological activity of phenylpropionic acid isolated from a terrestrial Streptomycetes. Pol J Microbiol. 2007;56(3):191-7. [PubMed:18062653 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .