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Showing metabocard for mono-Benzyl malonate (HMDB0059721)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-01-09 12:11:23 UTC
Update Date2023-02-21 17:29:15 UTC
HMDB IDHMDB0059721
Secondary Accession Numbers
  • HMDB59721
Metabolite Identification
Common Namemono-Benzyl malonate
Descriptionmono-Benzyl malonate (CAS Number 40204-26-0) is a white crystalline, with 47-51C melting point. Malonate is a competitive inhibitor of the enzyme succinate dehydrogenase: malonate binds to the active site of the enzyme without reacting, and so competes with succinate, the usual substrate of the enzyme. The observation that malonate is a competitive inhibitor of succinate dehydrogenase was used to deduce the structure of the active site in that enzyme.
Structure
Data?1677000555
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0059721 (mono-Benzyl malonate)

mono-Benzyl malonate
  Mrv0541 01091312052D          

 14 14  0  0  0  0            999 V2000
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  1 14  1  0  0  0  0
M  END
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3D MOL for HMDB0059721 (mono-Benzyl malonate)

HMDB0059721
     RDKit          3D
mono-Benzyl malonate
 24 24  0  0  0  0  0  0  0  0999 V2000
    4.3204   -0.1447   -1.2092 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3036    0.3388   -0.0612 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3971    1.0548    0.3846 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1469    0.1618    0.8166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0771   -0.6752    0.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4176   -1.7250   -0.3829 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7459   -0.3054    0.2202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2636   -1.1085   -0.3858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6044   -0.4576   -0.2282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3146   -0.5104    0.9427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5280    0.1100    1.0152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0462    0.7855   -0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3442    0.8501   -1.2579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1183    0.2139   -1.3048 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2970    2.0769    0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7063    1.1428    1.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3780   -0.3620    1.7858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2433   -2.1009    0.1075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0401   -1.2876   -1.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891   -1.0434    1.7699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0838    0.0632    1.9445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0088    1.2702   -0.0110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7335    1.3862   -2.1386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5720    0.2665   -2.2461 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  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14  9  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  8 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 13 23  1  0
 14 24  1  0
M  END
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3D SDF for HMDB0059721 (mono-Benzyl malonate)

mono-Benzyl malonate
  Mrv0541 01091312052D          

 14 14  0  0  0  0            999 V2000
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  1 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0059721

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CC(=O)OCC1=CC=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H10O4/c11-9(12)6-10(13)14-7-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,11,12)

> <INCHI_KEY>
CFLAHQSWDKNWPW-UHFFFAOYSA-N

> <FORMULA>
C10H10O4

> <MOLECULAR_WEIGHT>
194.184

> <EXACT_MASS>
194.057908808

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
19.115861319696734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(benzyloxy)-3-oxopropanoic acid

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
1.539249905

> <ALOGPS_LOGS>
-2.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.035690485775978

> <JCHEM_PKA_STRONGEST_BASIC>
-7.159684566418505

> <JCHEM_POLAR_SURFACE_AREA>
63.60000000000001

> <JCHEM_REFRACTIVITY>
48.3695

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.82e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(benzyloxy)-3-oxopropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0059721 (mono-Benzyl malonate)

HMDB0059721
     RDKit          3D
mono-Benzyl malonate
 24 24  0  0  0  0  0  0  0  0999 V2000
    4.3204   -0.1447   -1.2092 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3036    0.3388   -0.0612 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3971    1.0548    0.3846 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1469    0.1618    0.8166 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0771   -0.6752    0.1840 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4176   -1.7250   -0.3829 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7459   -0.3054    0.2202 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2636   -1.1085   -0.3858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6044   -0.4576   -0.2282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3146   -0.5104    0.9427 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5280    0.1100    1.0152 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0462    0.7855   -0.0687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3442    0.8501   -1.2579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1183    0.2139   -1.3048 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2970    2.0769    0.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7063    1.1428    1.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3780   -0.3620    1.7858 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2433   -2.1009    0.1075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0401   -1.2876   -1.4644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8891   -1.0434    1.7699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0838    0.0632    1.9445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0088    1.2702   -0.0110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7335    1.3862   -2.1386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5720    0.2665   -2.2461 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  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14  9  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  8 19  1  0
 10 20  1  0
 11 21  1  0
 12 22  1  0
 13 23  1  0
 14 24  1  0
M  END
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PDB for HMDB0059721 (mono-Benzyl malonate)

HEADER    PROTEIN                                 09-JAN-13   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: mono-Benzyl malonate                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JAN-13         0                                  
HETATM    1  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
CONECT    1    2    3   14                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14    1                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END
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3D PDB for HMDB0059721 (mono-Benzyl malonate)

COMPND    HMDB0059721
HETATM    1  O1  UNL     1       4.320  -0.145  -1.209  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.304   0.339  -0.061  1.00  0.00           C  
HETATM    3  O2  UNL     1       5.397   1.055   0.385  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.147   0.162   0.817  1.00  0.00           C  
HETATM    5  C3  UNL     1       2.077  -0.675   0.184  1.00  0.00           C  
HETATM    6  O3  UNL     1       2.418  -1.725  -0.383  1.00  0.00           O  
HETATM    7  O4  UNL     1       0.746  -0.305   0.220  1.00  0.00           O  
HETATM    8  C4  UNL     1      -0.264  -1.109  -0.386  1.00  0.00           C  
HETATM    9  C5  UNL     1      -1.604  -0.458  -0.228  1.00  0.00           C  
HETATM   10  C6  UNL     1      -2.315  -0.510   0.943  1.00  0.00           C  
HETATM   11  C7  UNL     1      -3.528   0.110   1.015  1.00  0.00           C  
HETATM   12  C8  UNL     1      -4.046   0.786  -0.069  1.00  0.00           C  
HETATM   13  C9  UNL     1      -3.344   0.850  -1.258  1.00  0.00           C  
HETATM   14  C10 UNL     1      -2.118   0.214  -1.305  1.00  0.00           C  
HETATM   15  H1  UNL     1       5.297   2.077   0.461  1.00  0.00           H  
HETATM   16  H2  UNL     1       2.706   1.143   1.127  1.00  0.00           H  
HETATM   17  H3  UNL     1       3.378  -0.362   1.786  1.00  0.00           H  
HETATM   18  H4  UNL     1      -0.243  -2.101   0.107  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.040  -1.288  -1.464  1.00  0.00           H  
HETATM   20  H6  UNL     1      -1.889  -1.043   1.770  1.00  0.00           H  
HETATM   21  H7  UNL     1      -4.084   0.063   1.945  1.00  0.00           H  
HETATM   22  H8  UNL     1      -5.009   1.270  -0.011  1.00  0.00           H  
HETATM   23  H9  UNL     1      -3.734   1.386  -2.139  1.00  0.00           H  
HETATM   24  H10 UNL     1      -1.572   0.267  -2.246  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7    8
CONECT    8    9   18   19
CONECT    9   10   10   14
CONECT   10   11   20
CONECT   11   12   12   21
CONECT   12   13   22
CONECT   13   14   14   23
CONECT   14   24
END
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SMILES for HMDB0059721 (mono-Benzyl malonate)

OC(=O)CC(=O)OCC1=CC=CC=C1
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INCHI for HMDB0059721 (mono-Benzyl malonate)

InChI=1S/C10H10O4/c11-9(12)6-10(13)14-7-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,11,12)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Benzyloxycarbonylacetic acidChEBI
Benzyl hemimalonateChEBI
Benzyl hydrogen malonateChEBI
Monobenzyl malonateChEBI
2-BenzyloxycarbonylacetateGenerator
Benzyl hemimalonic acidGenerator
Benzyl hydrogen malonic acidGenerator
Monobenzyl malonic acidGenerator
mono-Benzyl malonic acidGenerator
3-(Benzyloxy)-3-oxopropanoateHMDB
mono-Benzyl malonateChEBI
Chemical FormulaC10H10O4
Average Molecular Weight194.184
Monoisotopic Molecular Weight194.057908808
IUPAC Name3-(benzyloxy)-3-oxopropanoic acid
Traditional Name3-(benzyloxy)-3-oxopropanoic acid
CAS Registry Number40204-26-0
SMILES
OC(=O)CC(=O)OCC1=CC=CC=C1
InChI Identifier
InChI=1S/C10H10O4/c11-9(12)6-10(13)14-7-8-4-2-1-3-5-8/h1-5H,6-7H2,(H,11,12)
InChI KeyCFLAHQSWDKNWPW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzyloxycarbonyls. These are organic compounds containing a carbonyl group substituted with a benzyloxyl group.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzyloxycarbonyls
Direct ParentBenzyloxycarbonyls
Alternative Parents
Substituents
  • Benzyloxycarbonyl
  • 1,3-dicarbonyl compound
  • Dicarboxylic acid or derivatives
  • Carboxylic acid ester
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
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
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound181659
PDB IDNot Available
ChEBI ID84093
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available