MiMeDB: Showing metabocard for N-(3-O-phospho-D-ribulosyl)-cadaverine (MMDBc0056106)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:16:50 UTC

Update Date

2022-08-12 20:09:35 UTC

Metabolite ID

MMDBc0056106

Metabolite Identification

Common Name

N-(3-O-phospho-D-ribulosyl)-cadaverine

Description

CHEBI:144614 belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain. Based on a literature review very few articles have been published on CHEBI:144614.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222162D          

 22 21  0  0  1  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  0  0  0  0  0  0  0  0  0  0
   -1.0461   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1895   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3316   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0974   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9552   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8118   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2408   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5263   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9039   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3829   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.6697   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8118   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2408   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3993   -2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2243   -3.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0974   -3.4914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8118   -3.0789    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.2408   -2.2539    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5263   -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
  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 19  1  6  0  0  0
 20 16  1  0  0  0  0
 20 17  1  0  0  0  0
 20 18  2  0  0  0  0
 20 19  1  0  0  0  0
  9 21  1  1  0  0  0
 10 22  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056106

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H23N2O7P/c11-4-2-1-3-5-12-6-8(14)10(9(15)7-13)19-20(16,17)18/h9-10,12-13,15H,1-7,11H2,(H2,16,17,18)/t9-,10+/m1/s1

> <INCHI_KEY>
KIZNUUOCZFPQOU-ZJUUUORDSA-N

> <FORMULA>
C10H23N2O7P

> <MOLECULAR_WEIGHT>
314.275

> <EXACT_MASS>
314.124288087

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
30.204558999277346

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4R)-1-[(5-aminopentyl)amino]-4,5-dihydroxy-2-oxopentan-3-yl]oxy}phosphonic acid

> <JCHEM_LOGP>
-4.463651755399965

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
5.9391391941542295

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.9051553899044209

> <JCHEM_PKA_STRONGEST_BASIC>
9.964361551590004

> <JCHEM_POLAR_SURFACE_AREA>
162.33999999999997

> <JCHEM_REFRACTIVITY>
70.9651

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(3R,4R)-1-[(5-aminopentyl)amino]-4,5-dihydroxy-2-oxopentan-3-yl]oxyphosphonic acid

> <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      -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      -1.953  -2.667   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      -0.619  -3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.048  -3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.383  -3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.382  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.049  -2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.716  -3.437   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -7.287  -2.667   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.715  -2.667   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       8.717  -2.667   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       3.382  -1.127   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       6.049  -1.127   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.612  -4.414   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.152  -7.081   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.048  -6.517   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       4.716  -4.977   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0       3.382  -5.747   0.000  0.00  0.00           P+0
HETATM   21  H   UNK     0       6.049  -4.207   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       4.716  -1.897   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   21                                             
CONECT   10    8    9   19   22                                             
CONECT   11    4                                                            
CONECT   12    5    6                                                       
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   20                                                            
CONECT   17   20                                                            
CONECT   18   20                                                            
CONECT   19   10   20                                                       
CONECT   20   16   17   18   19                                             
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

C₁₀H₂₃N₂O₇P

Average Mass

314.275

Monoisotopic Mass

314.124288087

IUPAC Name

{[(3R,4R)-1-[(5-aminopentyl)amino]-4,5-dihydroxy-2-oxopentan-3-yl]oxy}phosphonic acid

Traditional Name

[(3R,4R)-1-[(5-aminopentyl)amino]-4,5-dihydroxy-2-oxopentan-3-yl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]([H])(OP(O)(O)=O)C(=O)CNCCCCCN

InChI Identifier

InChI=1S/C10H23N2O7P/c11-4-2-1-3-5-12-6-8(14)10(9(15)7-13)19-20(16,17)18/h9-10,12-13,15H,1-7,11H2,(H2,16,17,18)/t9-,10+/m1/s1

InChI Key

KIZNUUOCZFPQOU-ZJUUUORDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Monosaccharide
Beta-hydroxy ketone
Alpha-aminoketone
Secondary alcohol
Ketone
1,2-diol
Secondary amine
Secondary aliphatic amine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
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	-4.5	ChemAxon
pKa (Strongest Acidic)	0.91	ChemAxon
pKa (Strongest Basic)	9.96	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	162.34 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	70.97 m³·mol⁻¹	ChemAxon
Polarizability	30.2 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_13) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-10	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-10	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	Firmicutes	2	Human ; Human feces

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

138911152

PDB ID

Not Available

ChEBI ID

Not Available

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 N-(3-O-phospho-D-ribulosyl)-cadaverine (MMDBc0056106)

MOL for #<Metabolite:0x00007fdb7177bab0>

3D MOL for #<Metabolite:0x00007fdb7177bab0>

3D SDF for #<Metabolite:0x00007fdb7177bab0>

3D-SDF for #<Metabolite:0x00007fdb7177bab0>

PDB for #<Metabolite:0x00007fdb7177bab0>

3D PDB for #<Metabolite:0x00007fdb7177bab0>

SMILES for #<Metabolite:0x00007fdb7177bab0>

INCHI for #<Metabolite:0x00007fdb7177bab0>

Structure for #<Metabolite:0x00007fdb7177bab0>

3D Structure for #<Metabolite:0x00007fdb7177bab0>