MiMeDB: Showing metabocard for 2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate (MMDBc0054157)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:26 UTC

Update Date

2022-09-01 02:27:33 UTC

Metabolite ID

MMDBc0054157

Metabolite Identification

Common Name

2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041518252D          
 
 13 12  0  0  1  0            999 V2000
    7.2189  -12.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9334  -12.8290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6479  -12.4165    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.3624  -12.8290    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0768  -12.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7914  -12.8290    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.5058  -12.4165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2203  -12.8290    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9334  -13.6539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6479  -11.5916    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3624  -13.6541    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7914  -13.6539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.5058  -11.5915    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
  2  9  2  0  0  0  0
  3 10  1  1  0  0  0
  4 11  1  1  0  0  0
  6 12  1  1  0  0  0
  7 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054157

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO5/c1-3(9)6(11)5(10)2-4(8)7(12)13/h4-6,10-11H,2,8H2,1H3,(H,12,13)/t4-,5+,6+/m0/s1

> <INCHI_KEY>
IFMHGOADXGYWMO-KVQBGUIXSA-N

> <FORMULA>
C7H13NO5

> <MOLECULAR_WEIGHT>
191.183

> <EXACT_MASS>
191.079372523

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
17.727028532825233

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R,5S)-2-amino-4,5-dihydroxy-6-oxoheptanoic acid

> <ALOGPS_LOGP>
-2.90

> <JCHEM_LOGP>
-4.437952247721822

> <ALOGPS_LOGS>
-0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.433493157962726

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9466267973089453

> <JCHEM_PKA_STRONGEST_BASIC>
8.64704012231261

> <JCHEM_POLAR_SURFACE_AREA>
120.85

> <JCHEM_REFRACTIVITY>
42.249900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.03e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R,5S)-2-amino-4,5-dihydroxy-6-oxoheptanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      13.475 -23.178   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.809 -23.948   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.143 -23.178   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.476 -23.948   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      18.810 -23.178   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      20.144 -23.948   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.478 -23.178   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      22.811 -23.948   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.809 -25.487   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      16.143 -21.638   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.476 -25.488   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      20.144 -25.487   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      21.478 -21.637   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5   11                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8   13                                                  
CONECT    8    7                                                            
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    6                                                            
CONECT   13    7                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

Synonyms

Value	Source
2-Amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid	ChEBI
2-Amino-3,7-dideoxy-D-threo-hept-6-ulosonate	Generator
2-Amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate	Generator

Molecular Formula

C₇H₁₃NO₅

Average Mass

191.183

Monoisotopic Mass

191.079372523

IUPAC Name

(2S,4R,5S)-2-amino-4,5-dihydroxy-6-oxoheptanoic acid

Traditional Name

(2S,4R,5S)-2-amino-4,5-dihydroxy-6-oxoheptanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C7H13NO5/c1-3(9)6(11)5(10)2-4(8)7(12)13/h4-6,10-11H,2,8H2,1H3,(H,12,13)/t4-,5+,6+/m0/s1

InChI Key

IFMHGOADXGYWMO-KVQBGUIXSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-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

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Medium-chain keto acid
Amino fatty acid
Hydroxy fatty acid
Acyloin
Beta-hydroxy ketone
Monosaccharide
Fatty acyl
Alpha-hydroxy ketone
1,3-aminoalcohol
Secondary alcohol
Amino acid
1,2-diol
Ketone
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxygen compound
Primary amine
Carbonyl group
Organonitrogen compound
Organic nitrogen compound
Amine
Organooxygen compound
Alcohol
Organic oxide
Organopnictogen compound
Primary aliphatic amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ketoaldonic acid derivative (CHEBI:51282 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	60.3 g/L	ALOGPS
logP	-2.9	ALOGPS
logP	-4.4	ChemAxon
logS	-0.5	ALOGPS
pKa (Strongest Acidic)	1.95	ChemAxon
pKa (Strongest Basic)	8.65	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	120.85 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	42.25 m³·mol⁻¹	ChemAxon
Polarizability	17.73 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	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_9) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00fv-0900000000-a70979bf27469eae6a91	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00fv-8900000000-7c4f78bc63167b98d9af	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00di-9200000000-f6e9908908022ec4e9af	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-006x-2900000000-1d77b54d2f9c51a030c2	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9700000000-5e002e68ce2f65d99a4f	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05fr-9300000000-72d03fdb2e602d1cdb4d	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014600	1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate	2,3-dioxopropyl phosphate	2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase	Synthesis	RHEA	34755880
MMDBr0014601	2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate	3-Dehydroquinate	3-dehydroquinate synthase	Synthesis	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
Bacteria	Aquificae	1
Archaea/Archaea	Euryarchaeota	26
Archaea/Archaea	Thaumarchaeota	2
Archaea/Archaea	Korarchaeota	1
Archaea	Euryarchaeota	2

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

Not Available

KEGG Compound ID

C16850

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25137912

PDB ID

Not Available

ChEBI ID

51282

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 2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate (MMDBc0054157)

MOL for #<Metabolite:0x00007fe2b4017040>

3D MOL for #<Metabolite:0x00007fe2b4017040>

3D SDF for #<Metabolite:0x00007fe2b4017040>

3D-SDF for #<Metabolite:0x00007fe2b4017040>

PDB for #<Metabolite:0x00007fe2b4017040>

3D PDB for #<Metabolite:0x00007fe2b4017040>

SMILES for #<Metabolite:0x00007fe2b4017040>

INCHI for #<Metabolite:0x00007fe2b4017040>

Structure for #<Metabolite:0x00007fe2b4017040>

3D Structure for #<Metabolite:0x00007fe2b4017040>