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Showing NP-Card for 3-Dehydroshikimic acid (NP0062933)

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Record Information
Version2.0
Created at2022-04-28 07:27:21 UTC
Updated at2022-04-28 07:27:21 UTC
NP-MRD IDNP0062933
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Dehydroshikimic acid
Description3-Dehydroshikimate belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. 3-Dehydroshikimate is an extremely weak basic (essentially neutral) compound (based on its pKa). 3-Dehydroshikimate exists in both E. 3-Dehydroshikimic acid is found in Escherichia coli. 3-Dehydroshikimic acid was first documented in 1999 (PMID: 10514257). Coli (prokaryote) and yeast (eukaryote).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0062933 (3-Dehydroshikimic acid)

 
  Mrv0541 02241222172D          
 
 12 12  0  0  1  0            999 V2000
   10.8206   -8.0597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5362   -8.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1088   -8.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8169   -7.2425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5362   -9.2988    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.1088   -9.2988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5249   -6.8320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1050   -6.8357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8206   -9.7169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2480   -9.7055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3969   -9.7055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8169  -10.5379    0.0000 O   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
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  1  0  0  0
  6 11  2  0  0  0  0
  9 12  1  6  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for NP0062933 (3-Dehydroshikimic acid)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.6447    2.0445    0.5669 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4553    0.8069    0.6328 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5633    0.0050    0.8146 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1477    0.2179    0.5265 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9949   -1.0938    0.6017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3251   -1.6989    0.4951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4732   -2.9372    0.7700 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4683   -0.8776    0.0730 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.6865   -1.4218    0.4104 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3208    0.4823    0.7276 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3622    1.2700    0.2936 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0265    1.1259    0.3296 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1973   -0.2217    0.0599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8490   -1.7584    0.7451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4404   -0.7444   -1.0294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3720   -1.1040   -0.2319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3478    0.3275    1.8205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0701    2.1828    0.0662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0716    1.3451   -0.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1123    2.0501    0.9378 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  2  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 18  1  0
 10 17  1  1
 12 19  1  0
 12 20  1  0
  5 14  1  0
  8 15  1  6
  9 16  1  0
  3 13  1  0
M  END
Download

3D SDF for NP0062933 (3-Dehydroshikimic acid)

 
  Mrv0541 02241222172D          
 
 12 12  0  0  1  0            999 V2000
   10.8206   -8.0597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5362   -8.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1088   -8.4703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8169   -7.2425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5362   -9.2988    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.1088   -9.2988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5249   -6.8320    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1050   -6.8357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8206   -9.7169    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.2480   -9.7055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3969   -9.7055    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8169  -10.5379    0.0000 O   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
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
  5 10  1  1  0  0  0
  6 11  2  0  0  0  0
  9 12  1  6  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062933

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CC(=CC(=O)[C@H]1O)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)/t5-,6-/m1/s1

> <INCHI_KEY>
SLWWJZMPHJJOPH-PHDIDXHHSA-N

> <FORMULA>
C7H8O5

> <MOLECULAR_WEIGHT>
172.1354

> <EXACT_MASS>
172.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
14.914686507045417

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.19

> <JCHEM_LOGP>
-1.024897902666667

> <ALOGPS_LOGS>
-0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.41661028782423

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2142420075706486

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2670456083440538

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
38.1936

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.37e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydroshikimic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0062933 (3-Dehydroshikimic acid)

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PDB for NP0062933 (3-Dehydroshikimic acid)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      20.198 -15.045   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      21.534 -15.811   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.870 -15.811   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.192 -13.519   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.534 -17.358   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.870 -17.358   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      21.513 -12.753   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      18.863 -12.760   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      20.198 -18.138   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      22.863 -18.117   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.541 -18.117   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      20.192 -19.671   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7    8                                                  
CONECT    5    2    9   10                                                  
CONECT    6    3   11    9                                                  
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5   12    6                                                  
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    9                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0062933 (3-Dehydroshikimic acid)
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SMILES for NP0062933 (3-Dehydroshikimic acid)
O[C@@H]1CC(=CC(=O)[C@H]1O)C(O)=O
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INCHI for NP0062933 (3-Dehydroshikimic acid)
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)/t5-,6-/m1/s1
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View in JSmol
Synonyms
ValueSource
(-)-3-Dehydroshikimic acidChEBI
5-DehydroshikimateChEBI
5-Dehydroshikimic acidChEBI
(-)-3-DehydroshikimateGenerator
3-Dehydroshikimic acidGenerator
3-DehydroshikimateChEBI
Chemical FormulaC7H8O5
Average Mass172.1354 Da
Monoisotopic Mass172.03717 Da
IUPAC Name(4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid
Traditional Name3-dehydroshikimic acid
CAS Registry NumberNot Available
SMILES
O[C@@H]1CC(=CC(=O)[C@H]1O)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)/t5-,6-/m1/s1
InChI KeySLWWJZMPHJJOPH-PHDIDXHHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Escherichia coliBacteria
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentCyclohexenones  
Alternative Parents
Substituents
  • Cyclohexenone
    • 

  • Secondary alcohol
    • 

  • 1,2-diol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
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
logP-1.2ALOGPS
logP-1ChemAxon
logS-0.1ALOGPS
pKa (Strongest Acidic)3.21ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area94.83 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity38.19 m³·mol⁻¹ChemAxon
Polarizability14.91 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDDB04347  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00019663  
Chemspider IDNot Available
KEGG Compound IDC02637  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Dehydroshikimic_acid  
METLIN IDNot Available
PubChem Compound439774  
PDB IDNot Available
ChEBI ID30918  
Good Scents IDNot Available
References
General References
  1. Li K, Frost JW: Microbial synthesis of 3-dehydroshikimic acid: a comparative analysis of D-xylose, L-arabinose, and D-glucose carbon sources. Biotechnol Prog. 1999 Sep-Oct;15(5):876-83. doi: 10.1021/bp990095c. [PubMed:10514257  ]