MiMeDB: Showing metabocard for pseudaminate (MMDBc0056277)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:21:35 UTC

Update Date

2025-10-07 16:09:42 UTC

Metabolite ID

MMDBc0056277

Metabolite Identification

Common Name

pseudaminate

Description

Pseudaminate is a metabolite classified within the broader category of amino sugars. Chemically, it is derived from the modification of amino sugar structures, which are integral components of various biological pathways. Pseudaminate is implicated in the modulation of bacterial cell walls and the human gut barrier, playing a role in the complex interplay between host and microbiome. This metabolite can influence the composition of the microbiome, potentially leading to significant changes in microbial populations and their associated functions (PMID:38868903 ). The presence of pseudaminate may affect the synthesis and integrity of cell wall components in bacteria, thereby impacting their viability and interaction with the host environment. Through these mechanisms, pseudaminate contributes to the intricate network of biochemical interactions that govern microbial ecology and host health.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222212D          

 28 28  0  0  1  0            999 V2000
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  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
   -1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    2.7717   -0.4887    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
    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   -0.8250    0.0000 H   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
  5  1  1  0  0  0  0
  6  2  1  4  0  0  0
  7  3  1  4  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  1  0  0  0
 11 10  1  0  0  0  0
 13  4  1  0  0  0  0
 13 12  1  1  0  0  0
 14  6  2  0  0  0  0
  9 14  1  6  0  0  0
 15  7  2  0  0  0  0
 10 15  1  6  0  0  0
  5 16  1  1  0  0  0
 17  6  1  0  0  0  0
 18  7  1  0  0  0  0
  8 19  1  1  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 13 22  1  6  0  0  0
 23 11  1  0  0  0  0
 23 13  1  0  0  0  0
  5 24  1  1  0  0  0
  8 25  1  6  0  0  0
  9 26  1  1  0  0  0
 10 27  1  6  0  0  0
 11 28  1  6  0  0  0
M  CHG  1  17  -1
M  END


  Mrv1652306172222212D          

 28 28  0  0  1  0            999 V2000
   -0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    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
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    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
   -0.7145   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  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
   -1.4289    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    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
    2.7717   -0.4887    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
    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   -0.8250    0.0000 H   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
  5  1  1  0  0  0  0
  6  2  1  4  0  0  0
  7  3  1  4  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  1  0  0  0
 11 10  1  0  0  0  0
 13  4  1  0  0  0  0
 13 12  1  1  0  0  0
 14  6  2  0  0  0  0
  9 14  1  6  0  0  0
 15  7  2  0  0  0  0
 10 15  1  6  0  0  0
  5 16  1  1  0  0  0
 17  6  1  0  0  0  0
 18  7  1  0  0  0  0
  8 19  1  1  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 13 22  1  6  0  0  0
 23 11  1  0  0  0  0
 23 13  1  0  0  0  0
  5 24  1  1  0  0  0
  8 25  1  6  0  0  0
  9 26  1  1  0  0  0
 10 27  1  6  0  0  0
 11 28  1  6  0  0  0
M  CHG  1  17  -1
M  END
> <DATABASE_ID>
MMDBc0056277

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C13H22N2O8/c1-5(16)9(14-6(2)17)11-10(15-7(3)18)8(19)4-13(22,23-11)12(20)21/h5,8-11,16,19,22H,4H2,1-3H3,(H,14,17)(H,15,18)(H,20,21)/p-1/t5-,8-,9-,10-,11-,13-/m0/s1

> <INCHI_KEY>
ZJOSXOOPEBJBMC-LJRWBPDUSA-M

> <FORMULA>
C13H21N2O8

> <MOLECULAR_WEIGHT>
333.318

> <EXACT_MASS>
333.130339224

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
31.245744059807542

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1S,2S)-1-[(2S,3S,4S,6S)-6-carboxy-4,6-dihydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-2-hydroxypropyl]ethanecarboximidate

> <JCHEM_LOGP>
-1.5692528171211038

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
5.486717707391844

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.208846575428846

> <JCHEM_PKA_STRONGEST_BASIC>
2.523396399848139

> <JCHEM_POLAR_SURFACE_AREA>
175.23

> <JCHEM_REFRACTIVITY>
84.93270000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1S,2S)-1-[(2S,3S,4S,6S)-6-carboxy-4,6-dihydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-2-hydroxypropyl]ethanecarboximidate

> <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      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.184   0.267   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -2.667   0.000   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      -1.334   2.310   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.174  -0.912   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.711   1.715   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       3.194  -1.447   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0      -0.000  -1.540   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       0.000   3.080   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.667  -1.540   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    7                                                            
CONECT    4    8   13                                                       
CONECT    5    1    9   16   24                                             
CONECT    6    2   14   17                                                  
CONECT    7    3   15   18                                                  
CONECT    8    4   10   19   25                                             
CONECT    9    5   11   14   26                                             
CONECT   10    8   11   15   27                                             
CONECT   11    9   10   23   28                                             
CONECT   12   13   20   21                                                  
CONECT   13    4   12   22   23                                             
CONECT   14    6    9                                                       
CONECT   15    7   10                                                       
CONECT   16    5                                                            
CONECT   17    6                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   11   13                                                       
CONECT   24    5                                                            
CONECT   25    8                                                            
CONECT   26    9                                                            
CONECT   27   10                                                            
CONECT   28   11                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   56    0
END

Synonyms

Value	Source
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonate	ChEBI
Pseudaminate anion	ChEBI
Pseudaminate(1-)	ChEBI
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-a-L-manno-non-2-ulopyranosonate	Generator
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-a-L-manno-non-2-ulopyranosonic acid	Generator
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid	Generator
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-non-2-ulopyranosonate	Generator
5,7-Bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-non-2-ulopyranosonic acid	Generator
Pseudaminic acid anion	Generator
Pseudaminic acid(1-)	Generator
Pseudaminic acid	Generator

Molecular Formula

C₁₃H₂₁N₂O₈

Average Mass

333.318

Monoisotopic Mass

333.130339224

IUPAC Name

N-[(1S,2S)-1-[(2S,3S,4S,6S)-6-carboxy-4,6-dihydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-2-hydroxypropyl]ethanecarboximidate

Traditional Name

N-[(1S,2S)-1-[(2S,3S,4S,6S)-6-carboxy-4,6-dihydroxy-3-[(1-hydroxyethylidene)amino]oxan-2-yl]-2-hydroxypropyl]ethanecarboximidate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C13H22N2O8/c1-5(16)9(14-6(2)17)11-10(15-7(3)18)8(19)4-13(22,23-11)12(20)21/h5,8-11,16,19,22H,4H2,1-3H3,(H,14,17)(H,15,18)(H,20,21)/p-1/t5-,8-,9-,10-,11-,13-/m0/s1

InChI Key

ZJOSXOOPEBJBMC-LJRWBPDUSA-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
Oxane
Pyran
Acetamide
Carboxamide group
Hemiacetal
Secondary carboxylic acid amide
Secondary alcohol
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organic oxide
Organic nitrogen compound
Alcohol
Organopnictogen compound
Organonitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

carbohydrate acid derivative anion (CHEBI:63282 )
monocarboxylic acid anion (CHEBI:63282 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.6	ChemAxon
pKa (Strongest Acidic)	3.21	ChemAxon
pKa (Strongest Basic)	2.52	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	175.23 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	84.93 m³·mol⁻¹	ChemAxon
Polarizability	31.25 Å³	ChemAxon
Number of Rings	1	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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	3	Human ; Human feces

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

26333074

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

56927739

PDB ID

Not Available

ChEBI ID

63282

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 pseudaminate (MMDBc0056277)

MOL for #<Metabolite:0x0000561537abfde0>

3D MOL for #<Metabolite:0x0000561537abfde0>

3D SDF for #<Metabolite:0x0000561537abfde0>

3D-SDF for #<Metabolite:0x0000561537abfde0>

PDB for #<Metabolite:0x0000561537abfde0>

3D PDB for #<Metabolite:0x0000561537abfde0>

SMILES for #<Metabolite:0x0000561537abfde0>

INCHI for #<Metabolite:0x0000561537abfde0>

Structure for #<Metabolite:0x0000561537abfde0>

3D Structure for #<Metabolite:0x0000561537abfde0>