NP-MRD: Showing NP-Card for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (NP0334311)

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Record Information

Version

2.0

Created at

2024-09-09 23:06:40 UTC

Updated at

2024-09-09 23:06:41 UTC

NP-MRD ID

NP0334311

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate

Description

2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate belongs to tricarboxylic acids and derivatives class of compounds. Those are carboxylic acids containing exactly three carboxyl groups. 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate is slightly soluble (in water) and a weakly acidic compound (based on its pKa). 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate can be found in a number of food items such as feijoa, german camomile, sugar apple, and rapini, which makes 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate a potential biomarker for the consumption of these food products.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05252301382D          

 23 23  0  0  0  0            999 V2000
    8.5737   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 O   0  0  0  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
    2.8579   -1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -2.8875    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  2  0  0  0  0
  2  4  1  0  0  0  0
  2  7  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  0  0  0  0
  5 10  1  0  0  0  0
  6 13  1  0  0  0  0
  6 23  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
  8 15  2  0  0  0  0
  9 12  1  0  0  0  0
  9 23  1  0  0  0  0
 10 16  2  0  0  0  0
 10 17  1  0  0  0  0
 11 12  1  0  0  0  0
 11 14  1  0  0  0  0
 12 18  1  0  0  0  0
 13 19  2  0  0  0  0
 13 20  1  0  0  0  0
 14 21  2  0  0  0  0
 14 22  1  0  0  0  0
M  CHG  3  17  -1  20  -1  22  -1
M  END
> <DATABASE_ID>
NP0334311

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(CC=C(C1C([O-])=O)C(=O)CCC([O-])=O)OC(=C)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1/C14H16O9/c1-6(13(19)20)23-9-4-2-7(8(15)3-5-10(16)17)11(12(9)18)14(21)22/h2,9,11-12,18H,1,3-5H2,(H,16,17)(H,19,20)(H,21,22)/p-3

> <INCHI_KEY>
JKJGLRGLOMRXFN-UHFFFAOYNA-K

> <FORMULA>
C14H13O9

> <MOLECULAR_WEIGHT>
325.251

> <EXACT_MASS>
325.057602738

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.924109269835085

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(1-carboxylatoeth-1-en-1-yl)oxy]-2-(3-carboxylatopropanoyl)-6-hydroxycyclohex-2-ene-1-carboxylate

> <JCHEM_LOGP>
-0.5422436176666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.692660845755071

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0757277830349627

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4187637794557157

> <JCHEM_POLAR_SURFACE_AREA>
166.92

> <JCHEM_REFRACTIVITY>
106.54310000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5-[(1-carboxylatoeth-1-en-1-yl)oxy]-2-(3-carboxylatopropanoyl)-6-hydroxycyclohex-2-ene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0      16.004  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  -1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.337  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.004  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669  -1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.003  -3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.338  -3.850   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -3.850   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.336   0.770   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      18.672  -3.080   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      17.338  -5.390   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0      14.670  -3.850   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    4    7                                                       
CONECT    3    5    8                                                       
CONECT    4    2    9                                                       
CONECT    5    3   10                                                       
CONECT    6    1   13   23                                                  
CONECT    7    2    8   11                                                  
CONECT    8    3    7   15                                                  
CONECT    9    4   12   23                                                  
CONECT   10    5   16   17                                                  
CONECT   11    7   12   14                                                  
CONECT   12    9   11   18                                                  
CONECT   13    6   19   20                                                  
CONECT   14   11   21   22                                                  
CONECT   15    8                                                            
CONECT   16   10                                                            
CONECT   17   10                                                            
CONECT   18   12                                                            
CONECT   19   13                                                            
CONECT   20   13                                                            
CONECT   21   14                                                            
CONECT   22   14                                                            
CONECT   23    6    9                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Value	Source
2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic acid	Generator

Chemical Formula

C₁₄H₁₃O₉

Average Mass

325.2510 Da

Monoisotopic Mass

325.05760 Da

IUPAC Name

5-[(1-carboxylatoeth-1-en-1-yl)oxy]-2-(3-carboxylatopropanoyl)-6-hydroxycyclohex-2-ene-1-carboxylate

Traditional Name

5-[(1-carboxylatoeth-1-en-1-yl)oxy]-2-(3-carboxylatopropanoyl)-6-hydroxycyclohex-2-ene-1-carboxylate

CAS Registry Number

Not Available

SMILES

OC1C(CC=C(C1C([O-])=O)C(=O)CCC([O-])=O)OC(=C)C([O-])=O

InChI Identifier

InChI=1/C14H16O9/c1-6(13(19)20)23-9-4-2-7(8(15)3-5-10(16)17)11(12(9)18)14(21)22/h2,9,11-12,18H,1,3-5H2,(H,16,17)(H,19,20)(H,21,22)/p-3

InChI Key

JKJGLRGLOMRXFN-UHFFFAOYNA-K

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
Gamma-keto acid
Beta-hydroxy acid
Hydroxy acid
Keto acid
Secondary alcohol
Ketone
Carboxylic acid
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organic anion
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

a small molecule (CPD-9924 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.54	ChemAxon
pKa (Strongest Acidic)	3.08	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	166.92 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	106.54 m³·mol⁻¹	ChemAxon
Polarizability	28.92 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Qin M, Song H, Dai X, Chen Y, Guo Z: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem J. 2018 Nov 30;475(22):3651-3667. doi: 10.1042/BCJ20180548. [PubMed:30341164 ]
Hailes HC, Rother D, Muller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M: Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J. 2013 Dec;280(24):6374-94. doi: 10.1111/febs.12496. Epub 2013 Sep 13. [PubMed:24034356 ]
Andrews FH, McLeish MJ: Using site-saturation mutagenesis to explore mechanism and substrate specificity in thiamin diphosphate-dependent enzymes. FEBS J. 2013 Dec;280(24):6395-411. doi: 10.1111/febs.12459. Epub 2013 Aug 23. [PubMed:23895593 ]
Jiang M, Chen X, Guo ZF, Cao Y, Chen M, Guo Z: Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli. Biochemistry. 2008 Mar 18;47(11):3426-34. doi: 10.1021/bi7023755. Epub 2008 Feb 20. [PubMed:18284213 ]
Jiang M, Chen M, Cao Y, Yang Y, Sze KH, Chen X, Guo Z: Determination of the stereochemistry of 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate, a key intermediate in menaquinone biosynthesis. Org Lett. 2007 Nov 8;9(23):4765-7. doi: 10.1021/ol702126m. Epub 2007 Oct 23. [PubMed:17956107 ]

Showing NP-Card for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (NP0334311)

MOL for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

3D MOL for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

3D SDF for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

3D-SDF for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

PDB for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

3D PDB for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

SMILES for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

INCHI for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

Structure for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)

3D Structure for NP0334311 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate)