MiMeDB: Showing metabocard for 3-Deoxy-D-manno-octulosonate (MMDBc0029999)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:50:05 UTC

Update Date

2022-08-31 17:38:32 UTC

Metabolite ID

MMDBc0029999

Metabolite Identification

Common Name

3-Deoxy-D-manno-octulosonate

Description

3-deoxy-D-manno-octulosonate is a member of the chemical class known as Octoses. These are monosaccahride compounds in which the sugar moiety is an octose (8 carbon atoms). 3-Deoxy-D-manno-octulosonic acid (KDO) is an eight-carbon sugar ubiquitous in Gram-negative bacterial lipopolysaccharides (LPS). (PMID 20801884 ) The enzyme 3-deoxy-D-manno-octulosonic acid (KDO) transferase is encoded by the kdtA gene of Escherichia coli and plays a key role in lipopolysaccharide biosynthesis.(PMID 1577828 ) KDO is an essential component of the lipopolysaccharide envelope in Gram-negative bacteria. (PMID 19726684 ) KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria. (PMID 10734095 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1533005141516362D          

 16 15  0  0  0  0            999 V2000
   -4.2857    0.7366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5712    1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8567    0.7366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1423    1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4278    0.7366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7133    1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0011    0.7366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7155    1.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4300    0.7366    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -5.0001    1.1491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5712    1.9741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8567   -0.0883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1423    1.9741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4278   -0.0883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0011   -0.0883    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7155    1.9741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 16  2  0  0  0  0
  7 15  2  0  0  0  0
  5 14  1  0  0  0  0
  3 12  1  0  0  0  0
  4 13  1  0  0  0  0
  2 11  1  0  0  0  0
  1 10  1  0  0  0  0
M  CHG  1   9  -1
M  END
> <DATABASE_ID>
MMDBc0029999

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/p-1

> <INCHI_KEY>
KYQCXUMVJGMDNG-UHFFFAOYSA-M

> <FORMULA>
C8H13O8

> <MOLECULAR_WEIGHT>
237.185

> <EXACT_MASS>
237.061590959

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
20.55884460846213

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5,6,7,8-pentahydroxy-2-oxooctanoate

> <ALOGPS_LOGP>
-2.12

> <JCHEM_LOGP>
-3.0357011243333334

> <ALOGPS_LOGS>
0.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.630062785724625

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.9038228877924785

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742108660118767

> <JCHEM_POLAR_SURFACE_AREA>
158.35

> <JCHEM_REFRACTIVITY>
59.078399999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5,6,7,8-pentahydroxy-2-oxooctanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0      -8.000   1.375   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.666   2.145   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.333   1.375   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.999   2.145   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.665   1.375   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.331   2.145   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.002   1.375   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.336   2.145   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.669   1.375   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      -9.334   2.145   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -6.666   3.685   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -5.333  -0.165   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.999   3.685   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -2.665  -0.165   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.002  -0.165   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.336   3.685   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3   11                                                  
CONECT    3    2    4   12                                                  
CONECT    4    3    5   13                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9   16                                                  
CONECT    9    8                                                            
CONECT   10    1                                                            
CONECT   11    2                                                            
CONECT   12    3                                                            
CONECT   13    4                                                            
CONECT   14    5                                                            
CONECT   15    7                                                            
CONECT   16    8                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
3-Deoxy-D-manno-octulosonic acid	Generator

Molecular Formula

C₈H₁₃O₈

Average Mass

237.185

Monoisotopic Mass

237.061590959

IUPAC Name

4,5,6,7,8-pentahydroxy-2-oxooctanoate

Traditional Name

4,5,6,7,8-pentahydroxy-2-oxooctanoate

CAS Registry Number

1069-03-0

SMILES

OCC(O)C(O)C(O)C(O)CC(=O)C([O-])=O

InChI Identifier

InChI=1S/C8H14O8/c9-2-5(12)7(14)6(13)3(10)1-4(11)8(15)16/h3,5-7,9-10,12-14H,1-2H2,(H,15,16)/p-1

InChI Key

KYQCXUMVJGMDNG-UHFFFAOYSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Octose monosaccharide
Medium-chain keto acid
Sugar acid
Alpha-keto acid
Beta-hydroxy ketone
Monosaccharide
Keto acid
1,2-diol
Secondary alcohol
Ketone
Carboxylic acid salt
Carboxylic acid derivative
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Organic oxide
Alcohol
Primary alcohol
Carbonyl group
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

a small molecule (KDO )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	263 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-3	ChemAxon
logS	0.01	ALOGPS
pKa (Strongest Acidic)	2.9	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	158.35 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	59.08 m³·mol⁻¹	ChemAxon
Polarizability	20.56 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
MMDBr0018382	3-Deoxy-D-manno-octulosonate 8-phosphate	3-Deoxy-D-manno-octulosonate	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC	Dephosphorylation	PathBank	31602464
MMDBr0018383	Cytidine triphosphate	CMP-3-Deoxy-D-manno-octulosonate	3-deoxy-manno-octulosonate cytidylyltransferase	Transfer of a cytidylyl group	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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

11575205

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

22706768

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 (MMDBc0029999)

MOL for #<Metabolite:0x00005645c9de4468>

3D MOL for #<Metabolite:0x00005645c9de4468>

3D SDF for #<Metabolite:0x00005645c9de4468>

3D-SDF for #<Metabolite:0x00005645c9de4468>

PDB for #<Metabolite:0x00005645c9de4468>

3D PDB for #<Metabolite:0x00005645c9de4468>

SMILES for #<Metabolite:0x00005645c9de4468>

INCHI for #<Metabolite:0x00005645c9de4468>

Structure for #<Metabolite:0x00005645c9de4468>

3D Structure for #<Metabolite:0x00005645c9de4468>