MiMeDB: Showing metabocard for 6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-) (MMDBc0049949)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:46:53 UTC

Update Date

2022-09-01 02:17:31 UTC

Metabolite ID

MMDBc0049949

Metabolite Identification

Common Name

6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041518592D          
 
 16 15  0  0  1  0            999 V2000
   15.5205  -11.9373    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.2400  -11.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8044  -11.5277    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.5205  -12.7669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9560  -11.9373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2400  -10.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0850  -11.9373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8044  -10.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9596  -12.7600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3689  -11.5277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7823  -12.7600    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   12.6529  -11.9373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3689  -10.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.6050  -12.7600    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7754  -13.5863    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7754  -11.9373    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  1  0  0  0
  2  5  1  0  0  0  0
  2  6  2  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  1  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  9 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  2  0  0  0  0
 11 14  1  0  0  0  0
 11 15  1  0  0  0  0
 11 16  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049949

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O9P/c7-3(1-5(9)10)6(11)4(8)2-15-16(12,13)14/h3,6-7,11H,1-2H2,(H,9,10)(H2,12,13,14)/t3-,6+/m1/s1

> <INCHI_KEY>
OLUPOJQIFXQXIT-CVYQJGLWSA-N

> <FORMULA>
C6H11O9P

> <MOLECULAR_WEIGHT>
258.119

> <EXACT_MASS>
258.014068932

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.894623734869022

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S)-3,4-dihydroxy-5-oxo-6-(phosphonooxy)hexanoic acid

> <ALOGPS_LOGP>
-2.38

> <JCHEM_LOGP>
-2.3551649246666666

> <ALOGPS_LOGS>
-1.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.878768830876437

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1776864139828334

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3401124929207926

> <JCHEM_POLAR_SURFACE_AREA>
161.59

> <JCHEM_REFRACTIVITY>
46.963899999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.60e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
DKHP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      28.972 -22.283   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.315 -21.518   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.635 -21.518   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      28.972 -23.832   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      31.651 -22.283   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      30.315 -19.969   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      26.292 -22.283   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      27.635 -19.969   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      31.658 -23.819   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      24.955 -21.518   0.000  0.00  0.00           C+0
HETATM   11  P   UNK     0      33.194 -23.819   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      23.619 -22.283   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      24.955 -19.969   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      34.729 -23.819   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      33.181 -25.361   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      33.181 -22.283   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1                                                            
CONECT    5    2    9                                                       
CONECT    6    2                                                            
CONECT    7    3   10                                                       
CONECT    8    3                                                            
CONECT    9    5   11                                                       
CONECT   10    7   12   13                                                  
CONECT   11    9   14   15   16                                             
CONECT   12   10                                                            
CONECT   13   10                                                            
CONECT   14   11                                                            
CONECT   15   11                                                            
CONECT   16   11                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
5-Dehydro-2-deoxy-D-gluconate 6-phosphate	ChEBI
6-Phospho-5-dehydro-2-deoxy-D-gluconate	ChEBI
DKHP	Kegg
5-Dehydro-2-deoxy-D-gluconic acid 6-phosphoric acid	Generator
2-Deoxy-5-keto-D-gluconate 6-phosphate	Generator
2-Deoxy-5-keto-D-gluconic acid 6-phosphoric acid	Generator
6-phospho-5-dehydro-2-Deoxy-D-gluconic acid	Generator

Molecular Formula

C₆H₁₁O₉P

Average Mass

258.119

Monoisotopic Mass

258.014068932

IUPAC Name

(3R,4S)-3,4-dihydroxy-5-oxo-6-(phosphonooxy)hexanoic acid

Traditional Name

DKHP

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H11O9P/c7-3(1-5(9)10)6(11)4(8)2-15-16(12,13)14/h3,6-7,11H,1-2H2,(H,9,10)(H2,12,13,14)/t3-,6+/m1/s1

InChI Key

OLUPOJQIFXQXIT-CVYQJGLWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Glycerone phosphates

Alternative Parents

Substituents

Glycerone phosphate
Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Monoalkyl phosphate
Acyloin
Beta-hydroxy ketone
Hydroxy acid
Fatty acyl
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Fatty acid
Alkyl phosphate
Alpha-hydroxy ketone
1,2-diol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Alcohol
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid phosphate (CHEBI:16925 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	16 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-2.4	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.18	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	46.96 m³·mol⁻¹	ChemAxon
Polarizability	19.89 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_16) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0007-4390000000-9782377b2bdb3a971e88	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0076-6930000000-2979fcf9021a22efcf6c	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-006y-9100000000-f85798ed8e4ed8063438	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0699-6950000000-f260983f44f707aa7ac0	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-44e3f86e79972ce1a1ae	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-9d1630d12cd4e5f15cdb	2019-02-23	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0006923	Adenosine triphosphate	ADP	Not Available	2-Deoxy-5-Keto-D-gluconate kinase	VMH	30371894
MMDBr0008272	6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)	Dihydroxyacetone phosphate	Not Available	2-Deoxy-5-keto-D-gluconate 6-phosphate aldolase	VMH	30371894
MMDBr0013192	6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)	Malonic semialdehyde	6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase	Aldol addition (or reverse)	RHEA	34755880
MMDBr0013223	5-dehydro-2-deoxy-D-gluconic acid	6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-)	5-dehydro-2-deoxygluconokinase	Phosphorylation	RHEA	34755880

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	Actinobacteria	30	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Proteobacteria	42	Human ; Human feces; Human pleural fluid plaque; Human dental plaque; Human nasal swab	Metabolic reconstruction
Bacteria	Firmicutes	88	Human feces; Human ; Human supragingival plaque; Catfish	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	3	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Tenericutes	3	Pig

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C06893

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

441202

PDB ID

Not Available

ChEBI ID

16925

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 6-phosphonato-5-dehydro-2-deoxy-D-gluconate(3-) (MMDBc0049949)

MOL for #<Metabolite:0x000055d246aca0a8>

3D MOL for #<Metabolite:0x000055d246aca0a8>

3D SDF for #<Metabolite:0x000055d246aca0a8>

3D-SDF for #<Metabolite:0x000055d246aca0a8>

PDB for #<Metabolite:0x000055d246aca0a8>

3D PDB for #<Metabolite:0x000055d246aca0a8>

SMILES for #<Metabolite:0x000055d246aca0a8>

INCHI for #<Metabolite:0x000055d246aca0a8>

Structure for #<Metabolite:0x000055d246aca0a8>

3D Structure for #<Metabolite:0x000055d246aca0a8>