MiMeDB: Showing metabocard for N(6)-(D-ribulosyl)-L-lysine (MMDBc0056197)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:19:16 UTC

Update Date

2025-10-07 16:09:39 UTC

Metabolite ID

MMDBc0056197

Metabolite Identification

Common Name

N(6)-(D-ribulosyl)-L-lysine

Description

N(6)-(D-ribulosyl)-L-lysine is a ribosylated amino acid, specifically classified as a modified amino acid. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential roles in metabolic pathways.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 22 21  0  0  1  0            999 V2000
    7.4763    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    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
    3.1895    1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.6197    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    2.6664    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    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
    3.9039    0.6039    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
   10.3342    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6197    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052    1.0164    0.0000 H   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
    3.1895    1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  7  1  0  0  0  0
  7 12  1  1  0  0  0
 13  4  1  0  0  0  0
 13  5  1  0  0  0  0
 14  6  1  0  0  0  0
 15  8  2  0  0  0  0
  9 16  1  1  0  0  0
 10 17  1  6  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
  7 20  1  1  0  0  0
  9 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  CHG  1  12   1
M  END
> <DATABASE_ID>
MMDBc0056197

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]([NH3+])(CCCCNCC(=O)[C@]([H])(O)[C@]([H])(O)CO)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H22N2O6/c12-7(11(18)19)3-1-2-4-13-5-8(15)10(17)9(16)6-14/h7,9-10,13-14,16-17H,1-6,12H2,(H,18,19)/p+1/t7-,9+,10-/m0/s1

> <INCHI_KEY>
SMNBVUPHZDTVSW-SFGNSQDASA-O

> <FORMULA>
C11H23N2O6

> <MOLECULAR_WEIGHT>
279.312

> <EXACT_MASS>
279.155062889

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
28.982866902042307

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S)-1-carboxy-5-{[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]amino}pentan-1-aminium

> <JCHEM_LOGP>
-4.846790795729175

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.547181784150785

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.242472745812361

> <JCHEM_PKA_STRONGEST_BASIC>
9.344807270465052

> <JCHEM_POLAR_SURFACE_AREA>
154.73

> <JCHEM_REFRACTIVITY>
77.21489999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-1-carboxy-5-{[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]amino}pentan-1-aminium

> <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      13.956   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.289   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.288   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      16.623   3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.957   2.667   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      16.623   4.977   0.000  0.00  0.00           N+1
HETATM   13  N   UNK     0       9.955   2.667   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       1.953   2.667   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.287   1.127   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.620   1.127   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       5.954   4.977   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      19.290   3.437   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      17.957   1.127   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0      16.623   1.897   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       4.620   4.207   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       5.954   1.897   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2   13                                                       
CONECT    5    8   13                                                       
CONECT    6    9   14                                                       
CONECT    7    3   11   12   20                                             
CONECT    8    5   10   15                                                  
CONECT    9    6   10   16   21                                             
CONECT   10    8    9   17   22                                             
CONECT   11    7   18   19                                                  
CONECT   12    7                                                            
CONECT   13    4    5                                                       
CONECT   14    6                                                            
CONECT   15    8                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   11                                                            
CONECT   19   11                                                            
CONECT   20    7                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₂₃N₂O₆

Average Mass

279.312

Monoisotopic Mass

279.155062889

IUPAC Name

(1S)-1-carboxy-5-{[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]amino}pentan-1-aminium

Traditional Name

(1S)-1-carboxy-5-{[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]amino}pentan-1-aminium

CAS Registry Number

Not Available

SMILES

[H][C@]([NH3+])(CCCCNCC(=O)[C@]([H])(O)[C@]([H])(O)CO)C(O)=O

InChI Identifier

InChI=1S/C11H22N2O6/c12-7(11(18)19)3-1-2-4-13-5-8(15)10(17)9(16)6-14/h7,9-10,13-14,16-17H,1-6,12H2,(H,18,19)/p+1/t7-,9+,10-/m0/s1

InChI Key

SMNBVUPHZDTVSW-SFGNSQDASA-O

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

L-alpha-amino acid
Pentose monosaccharide
Alpha-amino acid or derivatives
Alpha-amino acid
Medium-chain fatty acid
Hydroxy fatty acid
Amino fatty acid
Fatty acyl
Fatty acid
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Alpha-aminoketone
1,3-aminoalcohol
Amino acid
Secondary alcohol
Ketone
Carboxylic acid salt
Amino acid or derivatives
Secondary amine
Polyol
Monocarboxylic acid or derivatives
Secondary aliphatic amine
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.8	ChemAxon
pKa (Strongest Acidic)	2.24	ChemAxon
pKa (Strongest Basic)	9.34	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	154.73 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	77.21 m³·mol⁻¹	ChemAxon
Polarizability	28.98 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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
Bacteria	Firmicutes	1	Human ; Human feces
Bacteria/Eubacteria	Firmicutes	2	Human ; Human feces
Bacteria/Eubacteria	Deinococcus-thermus	1

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

138911146

PDB ID

Not Available

ChEBI ID

Not Available

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 N(6)-(D-ribulosyl)-L-lysine (MMDBc0056197)

MOL for #<Metabolite:0x0000561532f25ce0>

3D MOL for #<Metabolite:0x0000561532f25ce0>

3D SDF for #<Metabolite:0x0000561532f25ce0>

3D-SDF for #<Metabolite:0x0000561532f25ce0>

PDB for #<Metabolite:0x0000561532f25ce0>

3D PDB for #<Metabolite:0x0000561532f25ce0>

SMILES for #<Metabolite:0x0000561532f25ce0>

INCHI for #<Metabolite:0x0000561532f25ce0>

Structure for #<Metabolite:0x0000561532f25ce0>

3D Structure for #<Metabolite:0x0000561532f25ce0>