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Showing metabocard for 3-Dehydroquinic acid (HMDB0012710)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
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
Data?1676999870
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
Download

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