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Showing metabocard for 3-Dehydroquinic acid (HMDB0012710)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-07-25 00:05:48 UTC
Update Date2023-02-21 17:17:50 UTC
HMDB IDHMDB0012710
Secondary Accession Numbers
  • HMDB12710
Metabolite Identification
Common Name3-Dehydroquinic acid
Description3-Dehydroquinic acid belongs to the class of organic compounds known as alpha-hydroxy acids and derivatives. These are organic compounds containing a carboxylic acid substituted with a hydroxyl group on the adjacent carbon. 3-Dehydroquinic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). In most organisms, 3-dehydroquinic acid is synthesized from D-erythrose-4-phosphate in two steps. However, archaea genomes contain no orthologs for the genes that encode these first two steps. Instead, archaeabacteria appear to utilize an alternative pathway in which 3-dehydroquinic acid is synthesized from 6-deoxy-5-ketofructose-1-phosphate and L-aspartate-semialdehyde. These two compounds are first condensed to form 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate, which cyclizes to 3-dehydroquinic acid. From 3-dehydroquinic acid and on to chorismate, the archaeal pathway appears to be identical to the bacterial pathway.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012710 (3-Dehydroquinic acid)

  Mrv1652309042000362D          

 13 13  0  0  0  0            999 V2000
10000.1518 9999.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8661 9999.4913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.151810000.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.1518 9999.0784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9999.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7209 9997.4272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9998.2528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7208 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0064 9999.4913    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.0064 9998.6663    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.7208 9998.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9998.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9999.4913    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
 13  4  1  1  0  0  0
  9  5  1  6  0  0  0
 11  6  2  0  0  0  0
 10  7  1  1  0  0  0
M  END
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3D MOL for HMDB0012710 (3-Dehydroquinic acid)

HMDB0012710
     RDKit          3D
3-Dehydroquinic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
   -0.8911   -2.2625    1.3574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.4588    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7656   -1.2603    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886    0.2123    0.2879 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7864    0.5751    1.5961 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5010    0.4213   -0.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984    0.8805    0.8240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9606    0.1065   -1.3007 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    0.9884   -0.6200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2529    0.7966   -0.1100 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1603    1.5459   -0.8364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6802   -0.6564   -0.1778 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9358   -0.7911    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4820   -1.9240    0.5694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7893   -1.4098   -1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384    1.5631    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9202   -0.8391   -1.6600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    2.0664   -0.4705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2626    0.6794   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2512    1.0770    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    1.9923   -0.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7135   -0.9695   -1.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9551   -1.3333    1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  3 14  1  0
  3 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  1
 11 21  1  0
 12 22  1  6
 13 23  1  0
M  END
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3D SDF for HMDB0012710 (3-Dehydroquinic acid)

  Mrv1652309042000362D          

 13 13  0  0  0  0            999 V2000
10000.1518 9999.9041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.8661 9999.4913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.151810000.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.1518 9999.0784    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9999.9041    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7209 9997.4272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2909 9998.2528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.7208 9999.9037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.0064 9999.4913    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.0064 9998.6663    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9998.7208 9998.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9998.6663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.4353 9999.4913    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  8  9  1  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  1 13  1  0  0  0  0
 13  4  1  1  0  0  0
  9  5  1  6  0  0  0
 11  6  2  0  0  0  0
 10  7  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0012710

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1

> <INCHI_KEY>
WVMWZWGZRAXUBK-SYTVJDICSA-N

> <FORMULA>
C7H10O6

> <MOLECULAR_WEIGHT>
190.1507

> <EXACT_MASS>
190.047738052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
16.45823621642952

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexane-1-carboxylic acid

> <ALOGPS_LOGP>
-2.05

> <JCHEM_LOGP>
-2.0552498786666664

> <ALOGPS_LOGS>
0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.359570129279923

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.304489138555496

> <JCHEM_PKA_STRONGEST_BASIC>
-3.272742784069651

> <JCHEM_POLAR_SURFACE_AREA>
115.06000000000002

> <JCHEM_REFRACTIVITY>
38.6974

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydroquinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0012710 (3-Dehydroquinic acid)

HMDB0012710
     RDKit          3D
3-Dehydroquinic acid
 23 23  0  0  0  0  0  0  0  0999 V2000
   -0.8911   -2.2625    1.3574 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6389   -1.4588    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7656   -1.2603    0.0782 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0886    0.2123    0.2879 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7864    0.5751    1.5961 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5010    0.4213   -0.0326 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2984    0.8805    0.8240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9606    0.1065   -1.3007 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1503    0.9884   -0.6200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2529    0.7966   -0.1100 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1603    1.5459   -0.8364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6802   -0.6564   -0.1778 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9358   -0.7911    0.3729 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4820   -1.9240    0.5694 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7893   -1.4098   -1.0392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8384    1.5631    1.6545 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9202   -0.8391   -1.6600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998    2.0664   -0.4705 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2626    0.6794   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2512    1.0770    0.9624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7639    1.9923   -0.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7135   -0.9695   -1.2553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9551   -1.3333    1.1938 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  1
  4  6  1  0
  6  7  2  0
  6  8  1  0
  4  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12  2  1  0
  3 14  1  0
  3 15  1  0
  5 16  1  0
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  1
 11 21  1  0
 12 22  1  6
 13 23  1  0
M  END
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PDB for HMDB0012710 (3-Dehydroquinic acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8666.9508666.488   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8668.2838665.717   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8666.9508668.029   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8666.9508664.946   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8661.6108666.488   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8664.2798661.864   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8661.6108663.405   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.2798666.487   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8662.9458665.717   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8662.9458664.177   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8664.2798663.407   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8665.6138664.177   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8665.6138665.717   0.000  0.00  0.00           C+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4   13                                                            
CONECT    5    9                                                            
CONECT    6   11                                                            
CONECT    7   10                                                            
CONECT    8    9   13                                                       
CONECT    9    8   10    5                                                  
CONECT   10    9   11    7                                                  
CONECT   11   10   12    6                                                  
CONECT   12   11   13                                                       
CONECT   13    8   12    1    4                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END
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3D PDB for HMDB0012710 (3-Dehydroquinic acid)

COMPND    HMDB0012710
HETATM    1  O1  UNL     1      -0.891  -2.262   1.357  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.639  -1.459   0.492  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.766  -1.260   0.078  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.089   0.212   0.288  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.786   0.575   1.596  1.00  0.00           O  
HETATM    6  C4  UNL     1       2.501   0.421  -0.033  1.00  0.00           C  
HETATM    7  O3  UNL     1       3.298   0.880   0.824  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.961   0.106  -1.301  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.150   0.988  -0.620  1.00  0.00           C  
HETATM   10  C6  UNL     1      -1.253   0.797  -0.110  1.00  0.00           C  
HETATM   11  O5  UNL     1      -2.160   1.546  -0.836  1.00  0.00           O  
HETATM   12  C7  UNL     1      -1.680  -0.656  -0.178  1.00  0.00           C  
HETATM   13  O6  UNL     1      -2.936  -0.791   0.373  1.00  0.00           O  
HETATM   14  H1  UNL     1       1.482  -1.924   0.569  1.00  0.00           H  
HETATM   15  H2  UNL     1       0.789  -1.410  -1.039  1.00  0.00           H  
HETATM   16  H3  UNL     1       0.838   1.563   1.654  1.00  0.00           H  
HETATM   17  H4  UNL     1       2.920  -0.839  -1.660  1.00  0.00           H  
HETATM   18  H5  UNL     1       0.400   2.066  -0.470  1.00  0.00           H  
HETATM   19  H6  UNL     1       0.263   0.679  -1.677  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.251   1.077   0.962  1.00  0.00           H  
HETATM   21  H8  UNL     1      -2.764   1.992  -0.209  1.00  0.00           H  
HETATM   22  H9  UNL     1      -1.714  -0.969  -1.255  1.00  0.00           H  
HETATM   23  H10 UNL     1      -2.955  -1.333   1.194  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   12
CONECT    3    4   14   15
CONECT    4    5    6    9
CONECT    5   16
CONECT    6    7    7    8
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   11   12   20
CONECT   11   21
CONECT   12   13   22
CONECT   13   23
END
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SMILES for HMDB0012710 (3-Dehydroquinic acid)

O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O
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INCHI for HMDB0012710 (3-Dehydroquinic acid)

InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
5-Dehydroquinic acidChEBI
5-DehydroquinateKegg
3-DehydroquinateGenerator
3-Dehydroquinic acidGenerator, KEGG
Cyclohexan-1,4,5-triol-3-one-1-carboxylic acidHMDB
(1R,3R,4S)-1,3,4-Trihydroxy-5-oxocyclohexanecarboxylic acidHMDB
1,3,4-Trihydroxy-5-oxocyclohexanecarboxylic acidHMDB
Chemical FormulaC7H10O6
Average Molecular Weight190.1507
Monoisotopic Molecular Weight190.047738052
IUPAC Name(1R,3R,4S)-1,3,4-trihydroxy-5-oxocyclohexane-1-carboxylic acid
Traditional Name3-dehydroquinic acid
CAS Registry Number10534-44-8
SMILES
O[C@@H]1C[C@@](O)(CC(=O)[C@H]1O)C(O)=O
InChI Identifier
InChI=1S/C7H10O6/c8-3-1-7(13,6(11)12)2-4(9)5(3)10/h3,5,8,10,13H,1-2H2,(H,11,12)/t3-,5+,7-/m1/s1
InChI KeyWVMWZWGZRAXUBK-SYTVJDICSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha hydroxy acids and derivatives. These are organic compounds containing a carboxylic acid substituted with a hydroxyl group on the adjacent carbon.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassAlpha hydroxy acids and derivatives
Direct ParentAlpha hydroxy acids and derivatives
Alternative Parents
Substituents
  • Alpha-hydroxy acid
  • Cyclitol or derivatives
  • Cyclic alcohol
  • Tertiary alcohol
  • Cyclic ketone
  • Secondary alcohol
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Polyol
  • Monocarboxylic acid or derivatives
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic oxide
  • Organooxygen compound
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic 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 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 Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)FemaleEpithelial ovarian cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB03868
Phenol Explorer Compound IDNot Available
FooDB IDFDB029168
KNApSAcK IDC00019664
Chemspider ID388474
KEGG Compound IDC00944
BioCyc IDDEHYDROQUINATE
BiGG IDNot Available
Wikipedia Link3-Dehydroquinic_acid
METLIN IDNot Available
PubChem Compound439351
PDB IDDQA
ChEBI ID17947
Food Biomarker OntologyNot Available
VMH ID3DHQ
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Beta-enolase
General function:
Involved in magnesium ion binding
Specific function:
Appears to have a function in striated muscle development and regeneration.
Gene Name:
ENO3
Uniprot ID:
P13929
Molecular weight:
42248.03
Enzyme Details
2. Gamma-enolase
General function:
Involved in magnesium ion binding
Specific function:
Has neurotrophic and neuroprotective properties on a broad spectrum of central nervous system (CNS) neurons. Binds, in a calcium-dependent manner, to cultured neocortical neurons and promotes cell survival (By similarity).
Gene Name:
ENO2
Uniprot ID:
P09104
Molecular weight:
47268.125
Enzyme Details
3. Alpha-enolase
General function:
Involved in magnesium ion binding
Specific function:
Multifunctional enzyme that, as well as its role in glycolysis, plays a part in various processes such as growth control, hypoxia tolerance and allergic responses. May also function in the intravascular and pericellular fibrinolytic system due to its ability to serve as a receptor and activator of plasminogen on the cell surface of several cell-types such as leukocytes and neurons. Stimulates immunoglobulin production. MBP1 binds to the myc promoter and acts as a transcriptional repressor. May be a tumor suppressor.
Gene Name:
ENO1
Uniprot ID:
P06733
Molecular weight:
36927.84