NP-MRD: Showing NP-Card for kdpg intermediate (NP0297139)

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Record Information

Version

2.0

Created at

2022-09-10 07:12:11 UTC

Updated at

2022-09-10 07:12:11 UTC

NP-MRD ID

NP0297139

Secondary Accession Numbers

None

Natural Product Identification

Common Name

kdpg intermediate

Description

2-Keto-3-deoxy-6-phosphogluconic acid, also known as 2-dehydro-3-deoxy-D-gluconate 6-phosphate or 6-phospho-2-dehydro-3-deoxy-D-gluconate, belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain. 2-Keto-3-deoxy-6-phosphogluconic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). 2-Keto-3-deoxy-6-phosphogluconic acid exists in all living organisms, ranging from bacteria to humans. The 5-phospho derivative of 2-dehydro-D-gluconic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231219062D          

 16 15  0  0  1  0            999 V2000
   12.2997  -17.4671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0167  -17.0532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0167  -16.2282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7312  -17.4657    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4456  -17.0532    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.4456  -16.2282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1601  -17.4657    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.1601  -18.2907    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8746  -17.0532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.5891  -17.4657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.3036  -17.0532    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.3036  -16.2282    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0180  -17.4657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.0180  -16.6407    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2997  -18.2921    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5853  -17.0546    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  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
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
  1 15  2  0  0  0  0
  1 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0297139

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O9P/c7-3(1-4(8)6(10)11)5(9)2-15-16(12,13)14/h3,5,7,9H,1-2H2,(H,10,11)(H2,12,13,14)/t3-,5+/m0/s1

> <INCHI_KEY>
OVPRPPOVAXRCED-WVZVXSGGSA-N

> <FORMULA>
C6H11O9P

> <MOLECULAR_WEIGHT>
258.1199

> <EXACT_MASS>
258.014068462

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
20.166331383317747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S,5R)-4,5-dihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

> <ALOGPS_LOGP>
-2.36

> <JCHEM_LOGP>
-1.8985972716666666

> <ALOGPS_LOGS>
-1.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.98091974057207

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.479791419702818

> <JCHEM_PKA_STRONGEST_BASIC>
-3.266803065880614

> <JCHEM_POLAR_SURFACE_AREA>
161.59

> <JCHEM_REFRACTIVITY>
47.1892

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
kdpg intermediate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      22.959 -32.605   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.298 -31.833   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      24.298 -30.293   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      25.632 -32.603   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      26.965 -31.833   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      26.965 -30.293   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      28.299 -32.603   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      28.299 -34.143   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      29.633 -31.833   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      30.966 -32.603   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0      32.300 -31.833   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      32.300 -30.293   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      33.634 -32.603   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      33.634 -31.063   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      22.959 -34.145   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      21.626 -31.835   0.000  0.00  0.00           O+0
CONECT    1    2   15   16                                                  
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15    1                                                            
CONECT   16    1                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
2-Dehydro-3-deoxy-6-phospho-D-gluconate	ChEBI
2-Dehydro-3-deoxy-D-gluconate 6-phosphate	ChEBI
2-Keto-3-deoxy-6-phosphogluconate	ChEBI
3-Deoxy-D-erythro-hex-2-ulosonic acid 6-phosphate	ChEBI
6-Phospho-2-dehydro-3-deoxy-D-gluconate	ChEBI
KDPG Intermediate	ChEBI
2-Dehydro-3-deoxy-6-phospho-D-gluconic acid	Generator
2-Dehydro-3-deoxy-D-gluconic acid 6-phosphoric acid	Generator
3-Deoxy-D-erythro-hex-2-ulosonate 6-phosphate	Generator
3-Deoxy-D-erythro-hex-2-ulosonic acid 6-phosphoric acid	Generator
6-Phospho-2-dehydro-3-deoxy-D-gluconic acid	Generator
KDPG Intermediic acid	Generator
2-Dehydro-3-deoxy-D-gluconate-6-phosphate	HMDB
2-Keto-3-deoxy-6-p-gluconate	HMDB
2-Keto-3-deoxy-6-phospho-gluconate	HMDB
2-Keto-3-deoxygluconate-6-p	HMDB
6-p-2-K-3-Deo-gluconate	HMDB
6-Phospho-2-dehydro-3-deoxygluconate	HMDB
6-Phospho-2-keto-3-deoxygluconate	HMDB

Chemical Formula

C₆H₁₁O₉P

Average Mass

258.1199 Da

Monoisotopic Mass

258.01407 Da

IUPAC Name

(4S,5R)-4,5-dihydroxy-2-oxo-6-(phosphonooxy)hexanoic acid

Traditional Name

kdpg intermediate

CAS Registry Number

Not Available

SMILES

O[C@H](COP(O)(O)=O)[C@@H](O)CC(=O)C(O)=O

InChI Identifier

InChI=1S/C6H11O9P/c7-3(1-4(8)6(10)11)5(9)2-15-16(12,13)14/h3,5,7,9H,1-2H2,(H,10,11)(H2,12,13,14)/t3-,5+/m0/s1

InChI Key

OVPRPPOVAXRCED-WVZVXSGGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Medium-chain keto acids and derivatives

Direct Parent

Medium-chain keto acids and derivatives

Alternative Parents

Substituents

Medium-chain keto acid
Monoalkyl phosphate
Alpha-keto acid
Beta-hydroxy ketone
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Alpha-hydroxy ketone
Ketone
1,2-diol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Organic oxygen compound
Carbonyl group
Alcohol
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid phosphate (CHEBI:15925 )

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	-2.4	ALOGPS
logP	-1.9	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	161.59 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	47.19 m³·mol⁻¹	ChemAxon
Polarizability	20.17 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon