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Showing NP-Card for (3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid (NP0245887)

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Record Information
Version2.0
Created at2022-09-07 07:08:06 UTC
Updated at2022-09-07 07:08:06 UTC
NP-MRD IDNP0245887
Secondary Accession NumbersNone
Natural Product Identification
Common Name(3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid
Description(+)-5-Epi-Shikimic acid 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. (3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid is found in Pinus contorta. Based on a literature review very few articles have been published on (+)-5-epi-Shikimic acid.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)


  Mrv1652309072209082D          

 12 12  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  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  2  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  2  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  2  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  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
  4 12  1  0  0  0  0
M  END
Download

3D MOL for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
    3.2641   -1.3091   -0.2318 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6799   -0.2141   -0.1065 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3748    0.9606    0.0551 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2073   -0.1529   -0.1290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5901    1.0049    0.0035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8694    1.2022   -0.0016 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3312    1.7997    1.1657 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5755   -0.0600   -0.3470 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9414   -0.0127   -0.1573 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9484   -1.2778    0.3009 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9538   -1.2341    1.6718 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4236   -1.3825   -0.2993 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8076    1.3854   -0.7727 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2266    1.9116    0.1302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0727    1.9249   -0.8477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2659    2.7857    1.1211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4250   -0.2157   -1.4582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3644   -0.6651   -0.7974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5551   -2.1528   -0.0123 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4996   -0.4844    2.0821 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2771   -1.5189   -1.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9513   -2.2950    0.0402 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10 12  1  0
 12  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  8 10  1  0
 11 20  1  0
 10 19  1  1
 12 21  1  0
 12 22  1  0
  5 14  1  0
  6 15  1  6
  7 16  1  0
  8 17  1  6
  9 18  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)


  Mrv1652309072209082D          

 12 12  0  0  1  0            999 V2000
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  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  2  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  2  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  2  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  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  6  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 10 12  1  0  0  0  0
  4 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0245887

> <DATABASE_NAME>
NP-MRD

> <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-/m0/s1

> <INCHI_KEY>
JXOHGGNKMLTUBP-JKUQZMGJSA-N

> <FORMULA>
C7H10O5

> <MOLECULAR_WEIGHT>
174.152

> <EXACT_MASS>
174.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.642233631701007

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.640074077

> <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

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

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)

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PDB for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
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                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    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 NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)
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SMILES for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic acid)
O[C@@H]1CC(=C[C@H](O)[C@@H]1O)C(O)=O
Download
INCHI for NP0245887 ((3s,4r,5r)-3,4,5-trihydroxycyclohex-1-ene-1-carboxylic 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-/m0/s1
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View in JSmol
Synonyms
ValueSource
(+)-5-Epi-shikimateGenerator
Chemical FormulaC7H10O5
Average Mass174.1520 Da
Monoisotopic Mass174.05282 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
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-/m0/s1
InChI KeyJXOHGGNKMLTUBP-JKUQZMGJSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Pinus contortaLOTUS Database
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 DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID23089616  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound40970370  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]