MiMeDB: Showing metabocard for N(8),N'(8)-citryl-bis(spermidine) (MMDBc0056203)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:19:27 UTC

Update Date

2022-08-12 20:09:37 UTC

Metabolite ID

MMDBc0056203

Metabolite Identification

Common Name

N(8),N'(8)-citryl-bis(spermidine)

Description

N8,N'8-citryl-bis(spermidine) belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Based on a literature review a significant number of articles have been published on N8,N'8-citryl-bis(spermidine).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 31 30  0  0  0  0            999 V2000
   -5.2224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    6.8427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6368   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6349   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    7.5572    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.3513   -1.0164    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -5.2224    4.6993    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0789   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4599   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  1  1  0  0  0  0
 10  2  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14  4  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 20 19  1  0  0  0  0
 21  7  1  0  0  0  0
 22  8  1  0  0  0  0
 23  9  1  0  0  0  0
 23 11  1  0  0  0  0
 24 10  1  0  0  0  0
 24 12  1  0  0  0  0
 25 13  1  4  0  0  0
 25 17  2  0  0  0  0
 26 14  1  4  0  0  0
 26 18  2  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29 19  2  0  0  0  0
 30 19  1  0  0  0  0
 31 20  1  0  0  0  0
M  CHG  3  21   1  22   1  23   1
M  END


  Mrv1652306172222192D          

 31 30  0  0  0  0            999 V2000
   -5.2224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    6.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    6.8427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6368   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    5.4138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6349   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224    7.5572    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.3513   -1.0164    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -5.2224    4.6993    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8099    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0789   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4599   -1.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  1  1  0  0  0  0
 10  2  1  0  0  0  0
 11  5  1  0  0  0  0
 12  6  1  0  0  0  0
 13  3  1  0  0  0  0
 14  4  1  0  0  0  0
 17 15  1  0  0  0  0
 18 16  1  0  0  0  0
 20 15  1  0  0  0  0
 20 16  1  0  0  0  0
 20 19  1  0  0  0  0
 21  7  1  0  0  0  0
 22  8  1  0  0  0  0
 23  9  1  0  0  0  0
 23 11  1  0  0  0  0
 24 10  1  0  0  0  0
 24 12  1  0  0  0  0
 25 13  1  4  0  0  0
 25 17  2  0  0  0  0
 26 14  1  4  0  0  0
 26 18  2  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29 19  2  0  0  0  0
 30 19  1  0  0  0  0
 31 20  1  0  0  0  0
M  CHG  3  21   1  22   1  23   1
M  END
> <DATABASE_ID>
MMDBc0056203

> <DATABASE_NAME>
MIME

> <SMILES>
[NH3+]CCCNCCCCN=C(O)CC(O)(CC(O)=NCCCC[NH2+]CCC[NH3+])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H42N6O5/c21-7-5-11-23-9-1-3-13-25-17(27)15-20(31,19(29)30)16-18(28)26-14-4-2-10-24-12-6-8-22/h23-24,31H,1-16,21-22H2,(H,25,27)(H,26,28)(H,29,30)/p+3

> <INCHI_KEY>
TWSVXJTXJAEAHP-UHFFFAOYSA-Q

> <FORMULA>
C20H45N6O5

> <MOLECULAR_WEIGHT>
449.615

> <EXACT_MASS>
449.343497833

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
52.05989258123169

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3-azaniumylpropyl)[4-({3-[({4-[(3-azaniumylpropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-3-carboxy-1,3-dihydroxypropylidene}amino)butyl]azanium

> <JCHEM_LOGP>
-9.209950257332316

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
3

> <JCHEM_PKA>
4.046006190538783

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1658565175088307

> <JCHEM_PKA_STRONGEST_BASIC>
10.80028788609039

> <JCHEM_POLAR_SURFACE_AREA>
206.62999999999997

> <JCHEM_REFRACTIVITY>
154.20480000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
21

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3-ammoniopropyl)[4-({3-[({4-[(3-ammoniopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-3-carboxy-1,3-dihydroxypropylidene}amino)butyl]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      -9.748   6.105   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.746  -1.897   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.978   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -9.748  11.439   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.588  -1.897   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -8.978  12.773   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.922  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.978   7.438   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.413  -2.667   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.978  10.106   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.255  -2.667   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -9.748   3.437   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.414  -1.897   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.978  -0.564   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.415  -2.667   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -9.748   0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -7.081  -1.897   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0     -10.518  -3.231   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -9.748  -1.897   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -9.748  14.107   0.000  0.00  0.00           N+1
HETATM   22  N   UNK     0       6.256  -1.897   0.000  0.00  0.00           N+1
HETATM   23  N   UNK     0      -9.748   8.772   0.000  0.00  0.00           N+1
HETATM   24  N   UNK     0       0.921  -1.897   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      -8.978   2.104   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0      -5.747  -2.667   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0     -11.288   0.770   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -7.081  -0.357   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -9.748  -4.565   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0     -12.058  -3.231   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0     -11.082  -1.127   0.000  0.00  0.00           O+0
CONECT    1    3    9                                                       
CONECT    2    4   10                                                       
CONECT    3    1   13                                                       
CONECT    4    2   14                                                       
CONECT    5    7   11                                                       
CONECT    6    8   12                                                       
CONECT    7    5   21                                                       
CONECT    8    6   22                                                       
CONECT    9    1   23                                                       
CONECT   10    2   24                                                       
CONECT   11    5   23                                                       
CONECT   12    6   24                                                       
CONECT   13    3   25                                                       
CONECT   14    4   26                                                       
CONECT   15   17   20                                                       
CONECT   16   18   20                                                       
CONECT   17   15   25   27                                                  
CONECT   18   16   26   28                                                  
CONECT   19   20   29   30                                                  
CONECT   20   15   16   19   31                                             
CONECT   21    7                                                            
CONECT   22    8                                                            
CONECT   23    9   11                                                       
CONECT   24   10   12                                                       
CONECT   25   13   17                                                       
CONECT   26   14   18                                                       
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29   19                                                            
CONECT   30   19                                                            
CONECT   31   20                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   60    0
END

Synonyms

Not Available

Molecular Formula

C₂₀H₄₅N₆O₅

Average Mass

449.615

Monoisotopic Mass

449.343497833

IUPAC Name

(3-azaniumylpropyl)[4-({3-[({4-[(3-azaniumylpropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-3-carboxy-1,3-dihydroxypropylidene}amino)butyl]azanium

Traditional Name

(3-ammoniopropyl)[4-({3-[({4-[(3-ammoniopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-3-carboxy-1,3-dihydroxypropylidene}amino)butyl]azanium

CAS Registry Number

Not Available

SMILES

[NH3+]CCCNCCCCN=C(O)CC(O)(CC(O)=NCCCC[NH2+]CCC[NH3+])C(O)=O

InChI Identifier

InChI=1S/C20H42N6O5/c21-7-5-11-23-9-1-3-13-25-17(27)15-20(31,19(29)30)16-18(28)26-14-4-2-10-24-12-6-8-22/h23-24,31H,1-16,21-22H2,(H,25,27)(H,26,28)(H,29,30)/p+3

InChI Key

TWSVXJTXJAEAHP-UHFFFAOYSA-Q

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Branched fatty acid
Hydroxy fatty acid
Fatty amide
N-acyl-amine
Tertiary alcohol
Quaternary ammonium salt
Carboxamide group
Carboxylic acid salt
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Primary aliphatic amine
Organic salt
Hydrocarbon derivative
Amine
Organic oxide
Alcohol
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
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	-9.2	ChemAxon
pKa (Strongest Acidic)	3.17	ChemAxon
pKa (Strongest Basic)	10.8	ChemAxon
Physiological Charge	3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	206.63 Å²	ChemAxon
Rotatable Bond Count	21	ChemAxon
Refractivity	154.2 m³·mol⁻¹	ChemAxon
Polarizability	52.06 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

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
MMDBr0017365	Adenosine triphosphate	Adenosine monophosphate	Citryl-spermidine/3,4-dihydroxybenzoyl-citryl-spermidine:spermidine ligase	Ligation	RHEA	34755880
MMDBr0025832	N(8),N'(8)-citryl-bis(spermidine)	Hydrogen Ion	Petrobactin 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	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	1	Human

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44237191

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(8),N'(8)-citryl-bis(spermidine) (MMDBc0056203)

MOL for #<Metabolite:0x00007fa4ed6526a8>

3D MOL for #<Metabolite:0x00007fa4ed6526a8>

3D SDF for #<Metabolite:0x00007fa4ed6526a8>

3D-SDF for #<Metabolite:0x00007fa4ed6526a8>

PDB for #<Metabolite:0x00007fa4ed6526a8>

3D PDB for #<Metabolite:0x00007fa4ed6526a8>

SMILES for #<Metabolite:0x00007fa4ed6526a8>

INCHI for #<Metabolite:0x00007fa4ed6526a8>

Structure for #<Metabolite:0x00007fa4ed6526a8>

3D Structure for #<Metabolite:0x00007fa4ed6526a8>