MiMeDB: Showing metabocard for N-(D-ribulosyl)-cadaverine (MMDBc0056111)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:16:58 UTC

Update Date

2025-10-07 16:09:33 UTC

Metabolite ID

MMDBc0056111

Metabolite Identification

Common Name

N-(D-ribulosyl)-cadaverine

Description

N-(D-ribulosyl)-cadaverine is a polyamine derivative. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222162D          

 18 17  0  0  1  0            999 V2000
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2572   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5427   -1.7309    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8283   -2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    4.9717   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1138   -0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5427   -0.9059    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283   -2.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5427   -2.5559    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8283   -1.3184    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
  5  3  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 10  9  1  0  0  0  0
 11  4  1  0  0  0  0
 12  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  7  1  0  0  0  0
 14  8  2  0  0  0  0
  9 15  1  1  0  0  0
 10 16  1  6  0  0  0
  9 17  1  1  0  0  0
 10 18  1  6  0  0  0
M  CHG  2  11   1  12   1
M  END
> <DATABASE_ID>
MMDBc0056111

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]([H])(O)C(=O)C[NH2+]CCCCC[NH3+]

> <INCHI_IDENTIFIER>
InChI=1S/C10H22N2O4/c11-4-2-1-3-5-12-6-8(14)10(16)9(15)7-13/h9-10,12-13,15-16H,1-7,11H2/p+2/t9-,10+/m1/s1

> <INCHI_KEY>
BZKXSLSRJJQPEX-ZJUUUORDSA-P

> <FORMULA>
C10H24N2O4

> <MOLECULAR_WEIGHT>
236.311

> <EXACT_MASS>
236.172510101

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
26.33283774826174

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5-azaniumylpentyl)[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]azanium

> <JCHEM_LOGP>
-2.2375206859056087

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
14.018175193004055

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.014728475512536

> <JCHEM_PKA_STRONGEST_BASIC>
11.556900104971977

> <JCHEM_POLAR_SURFACE_AREA>
122.01

> <JCHEM_REFRACTIVITY>
82.7999

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5-ammoniopentyl)[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]azanium

> <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      -2.723  -4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.389  -3.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.055  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.612  -4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.947  -4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.946  -3.231   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.613  -3.231   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.279  -4.001   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -6.724  -3.231   0.000  0.00  0.00           N+1
HETATM   12  N   UNK     0       1.278  -3.231   0.000  0.00  0.00           N+1
HETATM   13  O   UNK     0       9.280  -3.231   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       3.946  -1.691   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.613  -1.691   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.279  -5.541   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       6.613  -4.771   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       5.279  -2.461   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2   11                                                       
CONECT    5    3   12                                                       
CONECT    6    8   12                                                       
CONECT    7    9   13                                                       
CONECT    8    6   10   14                                                  
CONECT    9    7   10   15   17                                             
CONECT   10    8    9   16   18                                             
CONECT   11    4                                                            
CONECT   12    5    6                                                       
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17    9                                                            
CONECT   18   10                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₂₄N₂O₄

Average Mass

236.311

Monoisotopic Mass

236.172510101

IUPAC Name

(5-azaniumylpentyl)[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]azanium

Traditional Name

(5-ammoniopentyl)[(3R,4R)-3,4,5-trihydroxy-2-oxopentyl]azanium

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(O)C(=O)C[NH2+]CCCCC[NH3+]

InChI Identifier

InChI=1S/C10H22N2O4/c11-4-2-1-3-5-12-6-8(14)10(16)9(15)7-13/h9-10,12-13,15-16H,1-7,11H2/p+2/t9-,10+/m1/s1

InChI Key

BZKXSLSRJJQPEX-ZJUUUORDSA-P

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

Pentose monosaccharide
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Alpha-aminoketone
1,3-aminoalcohol
Secondary alcohol
Ketone
Secondary amine
Polyol
Secondary aliphatic amine
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
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	-2.2	ChemAxon
pKa (Strongest Acidic)	8.01	ChemAxon
pKa (Strongest Basic)	11.56	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	122.01 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	82.8 m³·mol⁻¹	ChemAxon
Polarizability	26.33 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

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	Firmicutes	1	Human ; Human feces
Bacteria/Eubacteria	Firmicutes	1	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

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

138911150

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-(D-ribulosyl)-cadaverine (MMDBc0056111)

MOL for #<Metabolite:0x00007fadd05c1ef0>

3D MOL for #<Metabolite:0x00007fadd05c1ef0>

3D SDF for #<Metabolite:0x00007fadd05c1ef0>

3D-SDF for #<Metabolite:0x00007fadd05c1ef0>

PDB for #<Metabolite:0x00007fadd05c1ef0>

3D PDB for #<Metabolite:0x00007fadd05c1ef0>

SMILES for #<Metabolite:0x00007fadd05c1ef0>

INCHI for #<Metabolite:0x00007fadd05c1ef0>

Structure for #<Metabolite:0x00007fadd05c1ef0>

3D Structure for #<Metabolite:0x00007fadd05c1ef0>