MiMeDB: Showing metabocard for 2-amino-2-deoxy-D-gluconic acid (MMDBc0054156)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:24 UTC

Update Date

2024-04-30 20:51:48 UTC

Metabolite ID

MMDBc0054156

Metabolite Identification

Common Name

2-amino-2-deoxy-D-gluconic acid

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305062021442D          

 17 16  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0461    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  3  1  0  0  0  0
  3  7  1  6  0  0  0
  8  1  1  0  0  0  0
  2  9  1  1  0  0  0
  4 10  1  6  0  0  0
  5 11  1  6  0  0  0
 12  6  2  0  0  0  0
 13  6  1  0  0  0  0
  2 14  1  1  0  0  0
  3 15  1  6  0  0  0
  4 16  1  6  0  0  0
  5 17  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054156

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO6/c7-3(6(12)13)5(11)4(10)2(9)1-8/h2-5,8-11H,1,7H2,(H,12,13)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
UFYKDFXCZBTLOO-TXICZTDVSA-N

> <FORMULA>
C6H13NO6

> <MOLECULAR_WEIGHT>
195.1705

> <EXACT_MASS>
195.074287153

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.496941567620944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R)-2-amino-3,4,5,6-tetrahydroxyhexanoic acid

> <ALOGPS_LOGP>
-3.24

> <JCHEM_LOGP>
-5.777403946832564

> <ALOGPS_LOGS>
-0.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.827339282682512

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8132118690847614

> <JCHEM_PKA_STRONGEST_BASIC>
8.311694397405732

> <JCHEM_POLAR_SURFACE_AREA>
144.24

> <JCHEM_REFRACTIVITY>
39.9285

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.48e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R)-2-amino-3,4,5,6-tetrahydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-20         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       8.621   4.977   0.000  0.00  0.00           N+0
HETATM    8  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.955   1.127   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       4.620   4.207   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       8.621   1.897   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       7.287   4.207   0.000  0.00  0.00           H+0
CONECT    1    2    8                                                       
CONECT    2    1    4    9   14                                             
CONECT    3    5    6    7   15                                             
CONECT    4    2    5   10   16                                             
CONECT    5    3    4   11   17                                             
CONECT    6    3   12   13                                                  
CONECT    7    3                                                            
CONECT    8    1                                                            
CONECT    9    2                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    2                                                            
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    5                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

Synonyms

Value	Source
(3R,4S,5R)-3,4,5,6-Tetrahydroxy-D-norleucine	ChEBI
2-Amino-2-deoxy-D-gluconate	ChEBI
D-Glucosaminate	ChEBI
D-Glucosaminic acid	ChEBI
Glucosaminate	ChEBI
Glucosaminic acid	Generator
2-amino-2-Deoxygluconic acid	MeSH
Glucosaminic acid, (D)-isomer	MeSH
2-Amino-2-deoxy-D-gluconic acid	Generator

Molecular Formula

C₆H₁₃NO₆

Average Mass

195.1705

Monoisotopic Mass

195.074287153

IUPAC Name

(2R,3R,4S,5R)-2-amino-3,4,5,6-tetrahydroxyhexanoic acid

Traditional Name

(2R,3R,4S,5R)-2-amino-3,4,5,6-tetrahydroxyhexanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@](N)(C(O)=O)[C@@]([H])(O)[C@]([H])(O)[C@]([H])(O)CO

InChI Identifier

InChI=1S/C6H13NO6/c7-3(6(12)13)5(11)4(10)2(9)1-8/h2-5,8-11H,1,7H2,(H,12,13)/t2-,3-,4-,5-/m1/s1

InChI Key

UFYKDFXCZBTLOO-TXICZTDVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Medium-chain hydroxy acid
Medium-chain fatty acid
Amino fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Amino saccharide
Hydroxy acid
Fatty acyl
Fatty acid
Monosaccharide
1,3-aminoalcohol
Amino acid
Secondary alcohol
Carboxylic acid
Monocarboxylic acid or derivatives
Polyol
Primary alcohol
Alcohol
Primary aliphatic amine
Primary amine
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Amine
Organonitrogen compound
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

gluconic acid derivative (CHEBI:17784 )
Uronic acids (C03752 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	148 g/L	ALOGPS
logP	-3.2	ALOGPS
logP	-5.8	ChemAxon
logS	-0.12	ALOGPS
pKa (Strongest Acidic)	1.81	ChemAxon
pKa (Strongest Basic)	8.31	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	144.24 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	39.93 m³·mol⁻¹	ChemAxon
Polarizability	17.5 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (6 TMS)	splash10-014i-1971000000-4c7b13b18177452796c3	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (7 TMS)	splash10-0gb9-0971000000-6ac782a9b0b1633e1fd0	2014-06-16	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004j-1900000000-0712ceb85fa55f01c894	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03mi-9200000000-300491806cc9334e9632	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03fr-9100000000-629b5a6f7de414f97a8a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f8c-5900000000-1bac32b787ded4112352	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0mbi-9400000000-3a8506f381b6b46f24a6	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ab9-9000000000-9f3481cdeedbc29dac93	2019-02-23	View Spectrum

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

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	1	Human ; Human subgingival plaque

Exposure Sources

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

Not Available

KEGG Compound ID

C03752

BioCyc ID

GLUCOSAMINATE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

73563

PDB ID

Not Available

ChEBI ID

17784

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Simon-Manso Y, Marupaka R, Yan X, Liang Y, Telu KH, Mirokhin Y, Stein SE: Mass Spectrometry Fingerprints of Small-Molecule Metabolites in Biofluids: Building a Spectral Library of Recurrent Spectra for Urine Analysis. Anal Chem. 2019 Sep 17;91(18):12021-12029. doi: 10.1021/acs.analchem.9b02977. Epub 2019 Aug 30. [PubMed:31424920 ]

Showing metabocard for 2-amino-2-deoxy-D-gluconic acid (MMDBc0054156)

MOL for #<Metabolite:0x00007fdb71489708>

3D MOL for #<Metabolite:0x00007fdb71489708>

3D SDF for #<Metabolite:0x00007fdb71489708>

3D-SDF for #<Metabolite:0x00007fdb71489708>

PDB for #<Metabolite:0x00007fdb71489708>

3D PDB for #<Metabolite:0x00007fdb71489708>

SMILES for #<Metabolite:0x00007fdb71489708>

INCHI for #<Metabolite:0x00007fdb71489708>

Structure for #<Metabolite:0x00007fdb71489708>

3D Structure for #<Metabolite:0x00007fdb71489708>