MiMeDB: Showing metabocard for 2-Keto-3-deoxy-6-phosphogluconic acid (MMDBc0029637)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:35:37 UTC

Update Date

2024-04-30 19:39:52 UTC

Metabolite ID

MMDBc0029637

Metabolite Identification

Common Name

2-Keto-3-deoxy-6-phosphogluconic acid

Description

2-Keto-3-deoxy-6-phosphogluconic acid is a substrate for Fructose-bisphosphate aldolase A.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D 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>
MMDBc0029637

> <DATABASE_NAME>
MIME

> <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

COMPND    HMDB0001376
HETATM    1  O1  UNL     1       3.173   1.903   0.490  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.572   0.743   0.279  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.699   0.290   1.028  1.00  0.00           O  
HETATM    4  C2  UNL     1       3.015  -0.213  -0.649  1.00  0.00           C  
HETATM    5  O3  UNL     1       3.532  -1.333  -0.735  1.00  0.00           O  
HETATM    6  C3  UNL     1       1.860   0.164  -1.455  1.00  0.00           C  
HETATM    7  C4  UNL     1       0.560   0.213  -0.751  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.649   1.170   0.299  1.00  0.00           O  
HETATM    9  C5  UNL     1       0.135  -1.057  -0.073  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.016  -2.049  -1.030  1.00  0.00           O  
HETATM   11  C6  UNL     1      -1.132  -0.845   0.728  1.00  0.00           C  
HETATM   12  O6  UNL     1      -2.206  -0.466  -0.061  1.00  0.00           O  
HETATM   13  P1  UNL     1      -3.592  -0.222   0.870  1.00  0.00           P  
HETATM   14  O7  UNL     1      -3.424  -0.671   2.286  1.00  0.00           O  
HETATM   15  O8  UNL     1      -4.890  -0.957   0.082  1.00  0.00           O  
HETATM   16  O9  UNL     1      -3.832   1.472   0.933  1.00  0.00           O  
HETATM   17  H1  UNL     1       5.619   0.282   0.633  1.00  0.00           H  
HETATM   18  H2  UNL     1       1.991   1.165  -1.961  1.00  0.00           H  
HETATM   19  H3  UNL     1       1.808  -0.545  -2.335  1.00  0.00           H  
HETATM   20  H4  UNL     1      -0.207   0.610  -1.434  1.00  0.00           H  
HETATM   21  H5  UNL     1       0.494   2.080  -0.071  1.00  0.00           H  
HETATM   22  H6  UNL     1       0.884  -1.439   0.646  1.00  0.00           H  
HETATM   23  H7  UNL     1      -0.826  -1.978  -1.556  1.00  0.00           H  
HETATM   24  H8  UNL     1      -1.428  -1.725   1.298  1.00  0.00           H  
HETATM   25  H9  UNL     1      -0.925  -0.019   1.463  1.00  0.00           H  
HETATM   26  H10 UNL     1      -5.157  -0.343  -0.666  1.00  0.00           H  
HETATM   27  H11 UNL     1      -4.354   1.659   1.741  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   17
CONECT    4    5    5    6
CONECT    6    7   18   19
CONECT    7    8    9   20
CONECT    8   21
CONECT    9   10   11   22
CONECT   10   23
CONECT   11   12   24   25
CONECT   12   13
CONECT   13   14   14   15   16
CONECT   15   26
CONECT   16   27
END

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

Molecular Formula

C₆H₁₁O₉P

Average Mass

258.1199

Monoisotopic Mass

258.014068462

IUPAC Name

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

Traditional Name

kdpg intermediate

CAS Registry Number

27244-54-8

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

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	14.3 g/L	ALOGPS
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

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018408	2-Keto-3-deoxy-D-gluconic acid	2-Keto-3-deoxy-6-phosphogluconic acid	2-dehydro-3-deoxygluconokinase	Phosphorylation	PathBank	31602464
MMDBr0018409	2-Keto-3-deoxy-6-phosphogluconic acid	D-Glyceraldehyde 3-phosphate	KHG/KDPG aldolase	Aldol addition (or reverse)	PathBank	31602464
MMDBr0019102	6-phospho-2-dehydro-D-gluconic acid	2-Keto-3-deoxy-6-phosphogluconic acid	Phosphogluconate dehydratase	Hydration/dehydration of C-O bond	PathBank	31602464

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	14	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria/Eubacteria	Firmicutes	1	Human feces
Archaea	Crenarchaeota	2	Human feces
Archaea/Archaea	Crenarchaeota	2	Human feces
Archaea/Archaea	Euryarchaeota	3
Bacteria/Eubacteria	Deinococcus-thermus	1
Archaea/Archaea	nah	1
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria/Eubacteria	Spirochaetes	1	Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0001376

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

2-KETO-3-DEOXY-6-P-GLUCONATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6202

PubChem Compound

3080745

PDB ID

Not Available

ChEBI ID

15925

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Kersters K, De Ley J: The occurrence of the Entner-Doudoroff pathway in bacteria. Antonie Van Leeuwenhoek. 1968;34(4):393-408. doi: 10.1007/BF02046462. [PubMed:5304016 ]
Andreesen JR, Gottschalk G: The occurrence of a modified Entner-doudoroff pathway in Clostridium aceticum. Arch Mikrobiol. 1969;69(2):160-70. doi: 10.1007/BF00409760. [PubMed:5383859 ]

Showing metabocard for 2-Keto-3-deoxy-6-phosphogluconic acid (MMDBc0029637)

MOL for #<Metabolite:0x00007f91feb15e08>

3D MOL for #<Metabolite:0x00007f91feb15e08>

3D SDF for #<Metabolite:0x00007f91feb15e08>

3D-SDF for #<Metabolite:0x00007f91feb15e08>

PDB for #<Metabolite:0x00007f91feb15e08>

3D PDB for #<Metabolite:0x00007f91feb15e08>

SMILES for #<Metabolite:0x00007f91feb15e08>

INCHI for #<Metabolite:0x00007f91feb15e08>

Structure for #<Metabolite:0x00007f91feb15e08>

3D Structure for #<Metabolite:0x00007f91feb15e08>