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Showing metabocard for Shikimic acid (HMDB0003070)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 15:12:30 UTC
Update Date2023-05-30 20:55:52 UTC
HMDB IDHMDB0003070
Secondary Accession Numbers
  • HMDB03070
Metabolite Identification
Common NameShikimic acid
DescriptionShikimic acid, more commonly known as its anionic form shikimate, is a cyclohexene, a cyclitol and a cyclohexanecarboxylic acid. It is an important biochemical intermediate in plants and microorganisms. Its name comes from the Japanese flower shikimi (the Japanese star anise, Illicium anisatum), from which it was first isolated. Shikimic acid is a precursor for: the aromatic amino acids phenylalanine and tyrosine; indole, indole derivatives and tryptophan; many alkaloids and other aromatic metabolites; tannins; and lignin. In pharmaceutical industry, shikimic acid from chinese star anise is used as a base material for production of Tamiflu (oseltamivir). Although shikimic acid is present in most autotrophic organisms, it is a biosynthetic intermediate and generally found in very low concentrations.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0003070 (Shikimic acid)

  Mrv1652309272007412D          

 12 12  0  0  0  0            999 V2000
10000.442410000.1947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.1566 9999.7818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.442410001.0203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0114 9997.7176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.581310000.1947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.5813 9998.5433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.011310000.1943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2969 9999.7818    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.2969 9998.9567    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.0113 9998.5444    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.7258 9998.9567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7258 9999.7818    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
  7  8  1  0  0  0  0
  7 12  2  0  0  0  0
  8  9  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
  1 12  1  0  0  0  0
 10  4  1  1  0  0  0
  9  6  1  6  0  0  0
  8  5  1  6  0  0  0
M  END
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3D MOL for HMDB0003070 (Shikimic acid)

HMDB0003070
     RDKit          3D
Shikimic acid
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.1569    1.2230   -0.3238 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6356    0.0855   -0.2049 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4292   -1.0115    0.0899 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2191   -0.0496   -0.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5818   -1.2037   -0.2734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8851   -1.1527   -0.4868 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4843   -2.3836   -0.1987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5756   -0.0433    0.2453 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1235   -0.4766    1.4542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6709    1.1405    0.4234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3698    2.3430    0.4678 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3552    1.1182   -0.6870 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2028   -0.9208    0.7383 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1103   -2.1333   -0.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0156   -0.9299   -1.5892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6494   -2.8580   -1.0509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4645    0.3468   -0.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7456    0.2296    1.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1000    1.0307    1.3864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3928    2.6825    1.4093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1491    0.9015   -1.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    2.0615   -0.7356 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  1  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
  3 13  1  0
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  1
 11 20  1  0
 12 21  1  0
 12 22  1  0
M  END
Download

3D SDF for HMDB0003070 (Shikimic acid)

  Mrv1652309272007412D          

 12 12  0  0  0  0            999 V2000
10000.442410000.1947    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.1566 9999.7818    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.442410001.0203    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.0114 9997.7176    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.581310000.1947    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.5813 9998.5433    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.011310000.1943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2969 9999.7818    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.2969 9998.9567    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9999.0113 9998.5444    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.7258 9998.9567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7258 9999.7818    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
  7  8  1  0  0  0  0
  7 12  2  0  0  0  0
  8  9  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
  1 12  1  0  0  0  0
 10  4  1  1  0  0  0
  9  6  1  6  0  0  0
  8  5  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0003070

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1

> <INCHI_KEY>
JXOHGGNKMLTUBP-HSUXUTPPSA-N

> <FORMULA>
C7H10O5

> <MOLECULAR_WEIGHT>
174.1513

> <EXACT_MASS>
174.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.745882820787454

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid

> <ALOGPS_LOGP>
-1.70

> <JCHEM_LOGP>
-1.640074077

> <ALOGPS_LOGS>
0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.02368088868393

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.10331906960995

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2247789599777335

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
38.9603

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.06e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-shikimate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0003070 (Shikimic acid)

HMDB0003070
     RDKit          3D
Shikimic acid
 22 22  0  0  0  0  0  0  0  0999 V2000
    3.1569    1.2230   -0.3238 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6356    0.0855   -0.2049 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4292   -1.0115    0.0899 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2191   -0.0496   -0.3790 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5818   -1.2037   -0.2734 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8851   -1.1527   -0.4868 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4843   -2.3836   -0.1987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5756   -0.0433    0.2453 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1235   -0.4766    1.4542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6709    1.1405    0.4234 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3698    2.3430    0.4678 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3552    1.1182   -0.6870 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2028   -0.9208    0.7383 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1103   -2.1333   -0.0430 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0156   -0.9299   -1.5892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6494   -2.8580   -1.0509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4645    0.3468   -0.3336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7456    0.2296    1.7502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1000    1.0307    1.3864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3928    2.6825    1.4093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1491    0.9015   -1.6590 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9352    2.0615   -0.7356 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  1  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
  3 13  1  0
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  6
  9 18  1  0
 10 19  1  1
 11 20  1  0
 12 21  1  0
 12 22  1  0
M  END
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PDB for HMDB0003070 (Shikimic acid)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.4928667.030   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8668.8268666.259   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.4928668.571   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8664.8218662.406   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8662.1528667.030   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8662.1528663.947   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0    8664.8218667.029   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8663.4888666.259   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8663.4888664.719   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8664.8218663.949   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8666.1558664.719   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8666.1558666.259   0.000  0.00  0.00           C+0
CONECT    1    2    3   12                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4   10                                                            
CONECT    5    8                                                            
CONECT    6    9                                                            
CONECT    7    8   12                                                       
CONECT    8    7    9    5                                                  
CONECT    9    8   10    6                                                  
CONECT   10    9   11    4                                                  
CONECT   11   10   12                                                       
CONECT   12    7   11    1                                                  
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
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3D PDB for HMDB0003070 (Shikimic acid)

COMPND    HMDB0003070
HETATM    1  O1  UNL     1       3.157   1.223  -0.324  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.636   0.086  -0.205  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.429  -1.012   0.090  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.219  -0.050  -0.379  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.582  -1.204  -0.273  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.885  -1.153  -0.487  1.00  0.00           C  
HETATM    7  O3  UNL     1      -1.484  -2.384  -0.199  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.576  -0.043   0.245  1.00  0.00           C  
HETATM    9  O4  UNL     1      -2.123  -0.477   1.454  1.00  0.00           O  
HETATM   10  C6  UNL     1      -0.671   1.140   0.423  1.00  0.00           C  
HETATM   11  O5  UNL     1      -1.370   2.343   0.468  1.00  0.00           O  
HETATM   12  C7  UNL     1       0.355   1.118  -0.687  1.00  0.00           C  
HETATM   13  H1  UNL     1       4.203  -0.921   0.738  1.00  0.00           H  
HETATM   14  H2  UNL     1       1.110  -2.133  -0.043  1.00  0.00           H  
HETATM   15  H3  UNL     1      -1.016  -0.930  -1.589  1.00  0.00           H  
HETATM   16  H4  UNL     1      -1.649  -2.858  -1.051  1.00  0.00           H  
HETATM   17  H5  UNL     1      -2.464   0.347  -0.334  1.00  0.00           H  
HETATM   18  H6  UNL     1      -2.746   0.230   1.750  1.00  0.00           H  
HETATM   19  H7  UNL     1      -0.100   1.031   1.386  1.00  0.00           H  
HETATM   20  H8  UNL     1      -1.393   2.683   1.409  1.00  0.00           H  
HETATM   21  H9  UNL     1      -0.149   0.902  -1.659  1.00  0.00           H  
HETATM   22  H10 UNL     1       0.935   2.062  -0.736  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   13
CONECT    4    5    5   12
CONECT    5    6   14
CONECT    6    7    8   15
CONECT    7   16
CONECT    8    9   10   17
CONECT    9   18
CONECT   10   11   12   19
CONECT   11   20
CONECT   12   21   22
END
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SMILES for HMDB0003070 (Shikimic acid)

O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
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INCHI for HMDB0003070 (Shikimic acid)

InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC7H10O5
Average Molecular Weight174.1513
Monoisotopic Molecular Weight174.05282343
IUPAC Name(3R,4S,5R)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
Traditional Name(-)-shikimate
CAS Registry Number138-59-0
SMILES
O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
InChI Identifier
InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
InChI KeyJXOHGGNKMLTUBP-HSUXUTPPSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as shikimic acids and derivatves. These are cyclitols containing a cyclohexanecarboxylic acid substituted with three hydroxyl groups at positions 3, 4, and 5.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentShikimic acids and derivatves
Alternative Parents
Substituents
  • Shikimic acid or derivatives
  • Secondary alcohol
  • Polyol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point186 °CNot Available
Boiling Point400.00 to 401.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility150 mg/mL at 21 °CNot Available
LogP-2.220 (est)The Good Scents Company Information System
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker140.55130932474
[M+H]+Baker149.49930932474
[M-H]-Not Available138.0http://allccs.zhulab.cn/database/detail?ID=AllCCS00001845
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothProstate Cancer details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB003991
KNApSAcK IDC00001203
Chemspider ID8412
KEGG Compound IDC00493
BioCyc IDSHIKIMATE
BiGG IDNot Available
Wikipedia LinkShikimic_acid
METLIN ID338
PubChem Compound8742
PDB IDNot Available
ChEBI ID16119
Food Biomarker OntologyNot Available
VMH IDSKM
MarkerDB IDNot Available
Good Scents IDrw1282291
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Liu Y, Xie MX, Jiang M, Wang YD: Spectroscopic investigation of the interaction between human serum albumin and three organic acids. Spectrochim Acta A Mol Biomol Spectrosc. 2005 Jul;61(9):2245-51. [PubMed:15911418 ]
  2. Rose GA: Studies on the chemical nature of urinary chemiluminescence. Br J Urol. 1976 Feb;48(1):61-71. [PubMed:5168 ]