MiMeDB: Showing metabocard for 3-Deoxy-D-manno-octulosonate 8-phosphate (MMDBc0029998)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:03 UTC

Update Date

2022-08-31 17:38:31 UTC

Metabolite ID

MMDBc0029998

Metabolite Identification

Common Name

3-Deoxy-D-manno-octulosonate 8-phosphate

Description

3-deoxy-D-manno-octulosonate 8-phosphate is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose. KDO 8P is involved in the KDO biosynthetic pathway. 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) phosphatase, which catalyzes the hydrolysis of KDO 8-P to KDO and inorganic phosphate, is the last enzyme in the KDO biosynthetic pathway for which the gene has not been identified. (PMID 12639950 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082006182D          

 20 19  0  0  0  0            999 V2000
   -2.3330    0.9596    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1581    0.9596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5705    1.6741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1581    2.3886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3330    2.3886    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3955    1.6741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5706    0.2451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3956    0.2452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1582   -0.4693    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5707   -1.1837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3332   -0.4693    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1583   -1.8982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5708   -2.6127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3333   -1.8983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3958   -2.6126    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -3.1583   -3.3272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9205    3.1030    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6232    3.4157    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0616    2.7011    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4962    3.7834    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  2  7  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
  3  6  1  0  0  0  0
  5  4  1  0  0  0  0
  2  1  1  0  0  0  0
  7  8  1  0  0  0  0
  9 11  1  0  0  0  0
 12 14  2  0  0  0  0
 13 16  2  0  0  0  0
 13 15  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 20  1  0  0  0  0
 17 19  1  0  0  0  0
M  CHG  3  15  -1  19  -1  20  -1
M  END
> <DATABASE_ID>
MMDBc0029998

> <DATABASE_NAME>
MIME

> <SMILES>
OC(COP([O-])([O-])=O)C(O)C(O)C(O)CC(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H15O11P/c9-3(1-4(10)8(14)15)6(12)7(13)5(11)2-19-20(16,17)18/h3,5-7,9,11-13H,1-2H2,(H,14,15)(H2,16,17,18)/p-3

> <INCHI_KEY>
RTNBXJBOAIDPME-UHFFFAOYSA-K

> <FORMULA>
C8H12O11P

> <MOLECULAR_WEIGHT>
315.148

> <EXACT_MASS>
315.013368944

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
24.222979139080696

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,6,7-tetrahydroxy-2-oxo-8-(phosphonooxy)octanoate

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-3.159267155666666

> <ALOGPS_LOGS>
-0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.0617402924129666

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4800967045224782

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2720378133123393

> <JCHEM_POLAR_SURFACE_AREA>
210.54

> <JCHEM_REFRACTIVITY>
67.7079

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.71e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,6,7-tetrahydroxy-2-oxo-8-(phosphonooxy)octanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  O   UNK     0      -4.355   1.791   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.895   1.791   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.665   3.125   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.895   4.459   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.355   4.459   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -8.205   3.125   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -6.665   0.458   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -8.205   0.458   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -5.895  -0.876   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -6.665  -2.210   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -4.355  -0.876   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -5.895  -3.543   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.665  -4.877   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -4.355  -3.543   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -8.205  -4.877   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      -5.895  -6.211   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0      -3.585   5.792   0.000  0.00  0.00           P+0
HETATM   18  O   UNK     0      -4.897   6.376   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.982   5.042   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      -2.793   7.062   0.000  0.00  0.00           O-1
CONECT    1    2                                                            
CONECT    2    3    7    1                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5                                                       
CONECT    5    4   17                                                       
CONECT    6    3                                                            
CONECT    7    2    9    8                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9   12                                                       
CONECT   11    9                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12   16   15                                                  
CONECT   14   12                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17    5   18   20   19                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

Synonyms

Value	Source
3-Deoxy-D-manno-octulosonic acid 8-phosphoric acid ⇥	Generator

Molecular Formula

C₈H₁₂O₁₁P

Average Mass

315.148

Monoisotopic Mass

315.013368944

IUPAC Name

4,5,6,7-tetrahydroxy-2-oxo-8-(phosphonooxy)octanoate

Traditional Name

4,5,6,7-tetrahydroxy-2-oxo-8-(phosphonooxy)octanoate

CAS Registry Number

Not Available

SMILES

OC(COP([O-])([O-])=O)C(O)C(O)C(O)CC(=O)C([O-])=O

InChI Identifier

InChI=1S/C8H15O11P/c9-3(1-4(10)8(14)15)6(12)7(13)5(11)2-19-20(16,17)18/h3,5-7,9,11-13H,1-2H2,(H,14,15)(H2,16,17,18)/p-3

InChI Key

RTNBXJBOAIDPME-UHFFFAOYSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Octose monosaccharide
Monosaccharide phosphate
Medium-chain keto acid
Sugar acid
Alpha-keto acid
Beta-hydroxy ketone
Keto acid
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Ketone
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Polyol
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (KDO-8P )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	47.1 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3.2	ChemAxon
logS	-0.89	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	210.54 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	67.71 m³·mol⁻¹	ChemAxon
Polarizability	24.22 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	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
MMDBr0007475	D-Arabinose 5-phosphate	3-Deoxy-D-manno-octulosonate 8-phosphate	Not Available	3-deoxy-D-manno-octulosonic-acid 8-phosphate synthease, reversible	VMH	30371894
MMDBr0018381	Phosphoenolpyruvic acid	Phosphate	2-dehydro-3-deoxyphosphooctonate aldolase	Aldol addition (or reverse)	PathBank	31602464
MMDBr0018382	Water	Phosphate	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC	Dephosphorylation	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	Proteobacteria	171	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	29	Pig ; Human feces; Human	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	113	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Actinobacteria	2	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction

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

24785208

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25244441

PDB ID

Not Available

ChEBI ID

Not Available

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 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for 3-Deoxy-D-manno-octulosonate 8-phosphate (MMDBc0029998)

MOL for #<Metabolite:0x00007f5abd3d8c30>

3D MOL for #<Metabolite:0x00007f5abd3d8c30>

3D SDF for #<Metabolite:0x00007f5abd3d8c30>

3D-SDF for #<Metabolite:0x00007f5abd3d8c30>

PDB for #<Metabolite:0x00007f5abd3d8c30>

3D PDB for #<Metabolite:0x00007f5abd3d8c30>

SMILES for #<Metabolite:0x00007f5abd3d8c30>

INCHI for #<Metabolite:0x00007f5abd3d8c30>

Structure for #<Metabolite:0x00007f5abd3d8c30>

3D Structure for #<Metabolite:0x00007f5abd3d8c30>