Showing metabocard for 3-Dehydro-shikimate (MMDBc0029769)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:40:51 UTC
Update Date2022-08-31 17:16:49 UTC
Metabolite IDMMDBc0029769
Metabolite Identification
Common Name3-Dehydro-shikimate
Description3-dehydro-shikimate is invovled in Chorismic acid biosynthesis. (KEGG)
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fece083e030>


  Mrv1652303082006182D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  4 12  1  0  0  0  0
M  CHG  1   2  -1
M  END
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3D MOL for #<Metabolite:0x00007fece083e030>

HMDB0304122
     RDKit          3D
3-dehydroshikimate
 19 19  0  0  0  0  0  0  0  0999 V2000
    3.1530    1.4238    0.0431 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5676    0.3640    0.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2665   -0.6737    0.8748 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.1528    0.2409    0.0748 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4624    1.2388   -0.4558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9558    1.0675   -0.6904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482    1.7564   -1.5610 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6629    0.0509    0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5500    0.4587    1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8676   -1.2397   -0.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8950   -1.5194   -1.4220 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5194   -1.0595    0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9545    2.1712   -0.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090   -0.0809   -0.1784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847    1.4513    1.4677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3445   -2.0540    0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6692   -0.6893   -1.9165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4915   -1.0617    1.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2194   -1.8451    0.0771 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
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12  4  1  0
  5 13  1  0
  8 14  1  0
  9 15  1  0
 10 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
M  CHG  1   3  -1
M  END
Download

3D SDF for #<Metabolite:0x00007fece083e030>


  Mrv1652303082006182D          

 12 12  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  1  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
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  4 12  1  0  0  0  0
M  CHG  1   2  -1
M  END
> <DATABASE_ID>
MMDBc0029769

> <DATABASE_NAME>
MIME

> <SMILES>
OC1CC(=CC(=O)C1O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H8O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,5-6,9-10H,2H2,(H,11,12)/p-1

> <INCHI_KEY>
SLWWJZMPHJJOPH-UHFFFAOYSA-M

> <FORMULA>
C7H7O5

> <MOLECULAR_WEIGHT>
171.129

> <EXACT_MASS>
171.029896905

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
14.58331268028746

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate

> <ALOGPS_LOGP>
-1.23

> <JCHEM_LOGP>
-1.024897902666667

> <ALOGPS_LOGS>
0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.416610287824234

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.21424200757065

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2670456083440538

> <JCHEM_POLAR_SURFACE_AREA>
97.66

> <JCHEM_REFRACTIVITY>
49.0307

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.56e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fece083e030>

HMDB0304122
     RDKit          3D
3-dehydroshikimate
 19 19  0  0  0  0  0  0  0  0999 V2000
    3.1530    1.4238    0.0431 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5676    0.3640    0.3272 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2665   -0.6737    0.8748 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.1528    0.2409    0.0748 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4624    1.2388   -0.4558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9558    1.0675   -0.6904 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5482    1.7564   -1.5610 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6629    0.0509    0.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5500    0.4587    1.4748 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8676   -1.2397   -0.0648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8950   -1.5194   -1.4220 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5194   -1.0595    0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9545    2.1712   -0.7105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7090   -0.0809   -0.1784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847    1.4513    1.4677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3445   -2.0540    0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6692   -0.6893   -1.9165 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4915   -1.0617    1.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2194   -1.8451    0.0771 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
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10 12  1  0
 12  4  1  0
  5 13  1  0
  8 14  1  0
  9 15  1  0
 10 16  1  0
 11 17  1  0
 12 18  1  0
 12 19  1  0
M  CHG  1   3  -1
M  END
Download

PDB for #<Metabolite:0x00007fece083e030>

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O-1
HETATM    3  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    3    4                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5   12                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    4                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for #<Metabolite:0x00007fece083e030>

COMPND    HMDB0304122
HETATM    1  O1  UNL     1       3.153   1.424   0.043  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.568   0.364   0.327  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.267  -0.674   0.875  1.00  0.00           O1-
HETATM    4  C2  UNL     1       1.153   0.241   0.075  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.462   1.239  -0.456  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.956   1.067  -0.690  1.00  0.00           C  
HETATM    7  O3  UNL     1      -1.548   1.756  -1.561  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.663   0.051   0.139  1.00  0.00           C  
HETATM    9  O4  UNL     1      -1.550   0.459   1.475  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.868  -1.240  -0.065  1.00  0.00           C  
HETATM   11  O5  UNL     1      -0.895  -1.519  -1.422  1.00  0.00           O  
HETATM   12  C7  UNL     1       0.519  -1.060   0.442  1.00  0.00           C  
HETATM   13  H1  UNL     1       0.954   2.171  -0.711  1.00  0.00           H  
HETATM   14  H2  UNL     1      -2.709  -0.081  -0.178  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.585   1.451   1.468  1.00  0.00           H  
HETATM   16  H4  UNL     1      -1.344  -2.054   0.510  1.00  0.00           H  
HETATM   17  H5  UNL     1      -0.669  -0.689  -1.916  1.00  0.00           H  
HETATM   18  H6  UNL     1       0.491  -1.062   1.570  1.00  0.00           H  
HETATM   19  H7  UNL     1       1.219  -1.845   0.077  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5    5   12
CONECT    5    6   13
CONECT    6    7    7    8
CONECT    8    9   10   14
CONECT    9   15
CONECT   10   11   12   16
CONECT   11   17
CONECT   12   18   19
END
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SMILES for #<Metabolite:0x00007fece083e030>

OC1CC(=CC(=O)C1O)C([O-])=O
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INCHI for #<Metabolite:0x00007fece083e030>

InChI=1S/C7H8O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,5-6,9-10H,2H2,(H,11,12)/p-1
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Synonyms
ValueSource
3-Dehydroshikimic acidGenerator
Molecular FormulaC7H7O5
Average Mass171.129
Monoisotopic Mass171.029896905
IUPAC Name4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate
Traditional Name4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylate
CAS Registry Number10457-99-5
SMILES
OC1CC(=CC(=O)C1O)C([O-])=O
InChI Identifier
InChI=1S/C7H8O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,5-6,9-10H,2H2,(H,11,12)/p-1
InChI KeySLWWJZMPHJJOPH-UHFFFAOYSA-M