MiMeDB: Showing metabocard for 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate (MMDBc0055361)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:50:05 UTC

Update Date

2022-08-12 20:09:21 UTC

Metabolite ID

MMDBc0055361

Metabolite Identification

Common Name

3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate

Description

3-deoxy-D-glycero-beta-D-galacto-nonulosonate, also known as beta-KDN(1-) or deamino-beta-neuraminate, belongs to the class of organic compounds known as c-glucuronides. These are glucuronides in which the aglycone is linked to the carbohydrate unit through a C-glycosidic bond. 3-deoxy-D-glycero-beta-D-galacto-nonulosonate is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 3-deoxy-D-glycero-beta-D-galacto-nonulosonate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221502D          

 23 23  0  0  1  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2414    0.1433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5236    0.9185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7717   -0.4887    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7111   -0.7752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  1  0  0  0
  9  1  1  0  0  0  0
  9  8  1  1  0  0  0
 10  2  1  0  0  0  0
  3 11  1  1  0  0  0
  4 12  1  6  0  0  0
  5 13  1  1  0  0  0
  6 14  1  1  0  0  0
 15  8  2  0  0  0  0
 16  8  1  0  0  0  0
  9 17  1  6  0  0  0
 18  7  1  0  0  0  0
 18  9  1  0  0  0  0
  3 19  1  6  0  0  0
  4 20  1  6  0  0  0
  5 21  1  1  0  0  0
  6 22  1  1  0  0  0
  7 23  1  6  0  0  0
M  CHG  1  16  -1
M  END
> <DATABASE_ID>
MMDBc0055361

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)[C@]1([H])O[C@@](O)(C[C@]([H])(O)[C@@]1([H])O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O9/c10-2-4(12)6(14)7-5(13)3(11)1-9(17,18-7)8(15)16/h3-7,10-14,17H,1-2H2,(H,15,16)/p-1/t3-,4+,5+,6+,7+,9-/m0/s1

> <INCHI_KEY>
CLRLHXKNIYJWAW-YOQZMRDMSA-M

> <FORMULA>
C9H15O9

> <MOLECULAR_WEIGHT>
267.211

> <EXACT_MASS>
267.072155643

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
23.380781339790005

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylate

> <JCHEM_LOGP>
-3.275902325333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.106537611051165

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.892075164751955

> <JCHEM_PKA_STRONGEST_BASIC>
-2.97421916261417

> <JCHEM_POLAR_SURFACE_AREA>
170.73999999999998

> <JCHEM_REFRACTIVITY>
63.517199999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.184   0.267   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.711   1.715   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.174  -0.912   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0       3.194  -1.447   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   19  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0      -0.000  -1.540   0.000  0.00  0.00           H+0
CONECT    1    3    9                                                       
CONECT    2    4   10                                                       
CONECT    3    1    5   11   19                                             
CONECT    4    2    6   12   20                                             
CONECT    5    3    7   13   21                                             
CONECT    6    4    7   14   22                                             
CONECT    7    5    6   18   23                                             
CONECT    8    9   15   16                                                  
CONECT    9    1    8   17   18                                             
CONECT   10    2                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    8                                                            
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18    7    9                                                       
CONECT   19    3                                                            
CONECT   20    4                                                            
CONECT   21    5                                                            
CONECT   22    6                                                            
CONECT   23    7                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

Synonyms

Value	Source
2-Keto-3-deoxy-D-glycero-D-galacto-NONONate	ChEBI
3-Deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate	ChEBI
beta-KDN(1-)	ChEBI
Deamino-beta-neuraminate	ChEBI
2-Keto-3-deoxy-D-glycero-D-galacto-NONONic acid	Generator
3-Deoxy-D-glycero-b-D-galacto-non-2-ulopyranosonate	Generator
3-Deoxy-D-glycero-b-D-galacto-non-2-ulopyranosonic acid	Generator
3-Deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid	Generator
3-Deoxy-D-glycero-β-D-galacto-non-2-ulopyranosonate	Generator
3-Deoxy-D-glycero-β-D-galacto-non-2-ulopyranosonic acid	Generator
b-KDN(1-)	Generator
Β-KDN(1-)	Generator
Deamino-b-neuraminate	Generator
Deamino-b-neuraminic acid	Generator
Deamino-beta-neuraminic acid	Generator
Deamino-β-neuraminate	Generator
Deamino-β-neuraminic acid	Generator
3-Deoxy-D-glycero-b-D-galacto-nonulosonate	Generator
3-Deoxy-D-glycero-b-D-galacto-nonulosonic acid	Generator
3-Deoxy-D-glycero-beta-D-galacto-nonulosonic acid	Generator
3-Deoxy-D-glycero-β-D-galacto-nonulosonate	Generator
3-Deoxy-D-glycero-β-D-galacto-nonulosonic acid	Generator

Molecular Formula

C₉H₁₅O₉

Average Mass

267.211

Monoisotopic Mass

267.072155643

IUPAC Name

(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylate

Traditional Name

(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)[C@]1([H])O[C@@](O)(C[C@]([H])(O)[C@@]1([H])O)C([O-])=O

InChI Identifier

InChI=1S/C9H16O9/c10-2-4(12)6(14)7-5(13)3(11)1-9(17,18-7)8(15)16/h3-7,10-14,17H,1-2H2,(H,15,16)/p-1/t3-,4+,5+,6+,7+,9-/m0/s1

InChI Key

CLRLHXKNIYJWAW-YOQZMRDMSA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as c-glucuronides. These are glucuronides in which the aglycone is linked to the carbohydrate unit through a C-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

C-glucuronides

Alternative Parents

Substituents

C-glucuronide
C-glycosyl compound
Glycosyl compound
Monosaccharide
Oxane
Pyran
Hemiacetal
Secondary alcohol
Polyol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid
Carboxylic acid derivative
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.3	ChemAxon
pKa (Strongest Acidic)	2.89	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	170.74 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	63.52 m³·mol⁻¹	ChemAxon
Polarizability	23.38 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0016434	3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate 9-phosphate	3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate	2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid phosphatase	Dephosphorylation	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	Bacteroidetes	1	Human ; Human feces

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

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

10340358

KEGG Compound ID

Not Available

BioCyc ID

CPD-10734

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23241229

PDB ID

Not Available

ChEBI ID

90988

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonate (MMDBc0055361)

MOL for #<Metabolite:0x00007f5abcef1730>

3D MOL for #<Metabolite:0x00007f5abcef1730>

3D SDF for #<Metabolite:0x00007f5abcef1730>

3D-SDF for #<Metabolite:0x00007f5abcef1730>

PDB for #<Metabolite:0x00007f5abcef1730>

3D PDB for #<Metabolite:0x00007f5abcef1730>

SMILES for #<Metabolite:0x00007f5abcef1730>

INCHI for #<Metabolite:0x00007f5abcef1730>

Structure for #<Metabolite:0x00007f5abcef1730>

3D Structure for #<Metabolite:0x00007f5abcef1730>