MiMeDB: Showing metabocard for N(8)-citryl-spermidine (MMDBc0056202)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:19:25 UTC

Update Date

2022-08-12 20:09:37 UTC

Metabolite ID

MMDBc0056202

Metabolite Identification

Common Name

N(8)-citryl-spermidine

Description

N-citryl-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 very few articles have been published on N-citryl-spermidine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222192D          

 22 21  0  0  0  0            999 V2000
   -0.9355   -1.0164    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
    1.9224   -1.0164    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
   -0.2211   -1.4289    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
   -2.3645   -1.0164    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
   -4.5079   -3.0789    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
   -3.7934   -3.4914    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3329   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5079   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3513   -1.0164    0.0000 N   0  0  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
   -3.0789   -1.4289    0.0000 N   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
   -3.7934   -4.3164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0789   -3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7454   -2.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7454   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6829   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  0  0  0  0
  7  2  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 13  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 12  1  0  0  0  0
 14  4  1  0  0  0  0
 15  5  1  0  0  0  0
 15  6  1  0  0  0  0
 16  7  1  4  0  0  0
 16 10  2  0  0  0  0
 17 10  1  0  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0056202

> <DATABASE_NAME>
MIME

> <SMILES>
NCCCNCCCCN=C(O)CC(O)(CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H25N3O6/c14-4-3-6-15-5-1-2-7-16-10(17)8-13(22,12(20)21)9-11(18)19/h15,22H,1-9,14H2,(H,16,17)(H,18,19)(H,20,21)

> <INCHI_KEY>
JJVVKHQEFSESNM-UHFFFAOYSA-N

> <FORMULA>
C13H25N3O6

> <MOLECULAR_WEIGHT>
319.358

> <EXACT_MASS>
319.174335537

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
33.244904760963465

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[({4-[(3-aminopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-2-hydroxybutanedioic acid

> <JCHEM_LOGP>
-7.369713935481689

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.8706947419982614

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.929876869681637

> <JCHEM_PKA_STRONGEST_BASIC>
10.499109968815567

> <JCHEM_POLAR_SURFACE_AREA>
165.47

> <JCHEM_REFRACTIVITY>
77.91409999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-[({4-[(3-aminopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-2-hydroxybutanedioic 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      -1.746  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.588  -1.897   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.922  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.413  -2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.255  -2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.415  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -8.415  -5.747   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -7.081  -1.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.081  -6.517   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -9.955  -4.207   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.415  -4.207   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       6.256  -1.897   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.921  -1.897   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -5.747  -2.667   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -7.081  -0.357   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.081  -8.057   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -5.747  -5.747   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0     -10.725  -5.541   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0     -10.725  -2.874   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -6.875  -4.207   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    7                                                       
CONECT    3    4    6                                                       
CONECT    4    3   14                                                       
CONECT    5    1   15                                                       
CONECT    6    3   15                                                       
CONECT    7    2   16                                                       
CONECT    8   10   13                                                       
CONECT    9   11   13                                                       
CONECT   10    8   16   17                                                  
CONECT   11    9   18   19                                                  
CONECT   12   13   20   21                                                  
CONECT   13    8    9   12   22                                             
CONECT   14    4                                                            
CONECT   15    5    6                                                       
CONECT   16    7   10                                                       
CONECT   17   10                                                            
CONECT   18   11                                                            
CONECT   19   11                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₃H₂₅N₃O₆

Average Mass

319.358

Monoisotopic Mass

319.174335537

IUPAC Name

2-[({4-[(3-aminopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-2-hydroxybutanedioic acid

Traditional Name

2-[({4-[(3-aminopropyl)amino]butyl}-C-hydroxycarbonimidoyl)methyl]-2-hydroxybutanedioic acid

CAS Registry Number

Not Available

SMILES

NCCCNCCCCN=C(O)CC(O)(CC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C13H25N3O6/c14-4-3-6-15-5-1-2-7-16-10(17)8-13(22,12(20)21)9-11(18)19/h15,22H,1-9,14H2,(H,16,17)(H,18,19)(H,20,21)

InChI Key

JJVVKHQEFSESNM-UHFFFAOYSA-N

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
Short-chain hydroxy acid
Hydroxy fatty acid
Alpha-hydroxy acid
Dicarboxylic acid or derivatives
Fatty amide
Hydroxy acid
N-acyl-amine
Tertiary alcohol
Amino acid or derivatives
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Secondary aliphatic amine
Carboxylic acid
Carboxylic acid derivative
Secondary amine
Primary aliphatic amine
Amine
Hydrocarbon derivative
Organic nitrogen compound
Organic oxide
Carbonyl group
Organic oxygen compound
Alcohol
Organonitrogen compound
Organooxygen compound
Primary amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

an aliphatic α,ω-diamine (CPD-11479 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-7.4	ChemAxon
pKa (Strongest Acidic)	2.93	ChemAxon
pKa (Strongest Basic)	10.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	165.47 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	77.91 m³·mol⁻¹	ChemAxon
Polarizability	33.24 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_1) - 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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0017364	Adenosine triphosphate	Adenosine monophosphate	Spermidine-citrate ligase	Ligation	RHEA	34755880
MMDBr0017365	Adenosine triphosphate	Adenosine monophosphate	Citryl-spermidine/3,4-dihydroxybenzoyl-citryl-spermidine:spermidine ligase	Ligation	RHEA	34755880
MMDBr0025833	N(8)-citryl-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

58837942

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44237228

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)-citryl-spermidine (MMDBc0056202)

MOL for #<Metabolite:0x00007fa4a3a0df08>

3D MOL for #<Metabolite:0x00007fa4a3a0df08>

3D SDF for #<Metabolite:0x00007fa4a3a0df08>

3D-SDF for #<Metabolite:0x00007fa4a3a0df08>

PDB for #<Metabolite:0x00007fa4a3a0df08>

3D PDB for #<Metabolite:0x00007fa4a3a0df08>

SMILES for #<Metabolite:0x00007fa4a3a0df08>

INCHI for #<Metabolite:0x00007fa4a3a0df08>

Structure for #<Metabolite:0x00007fa4a3a0df08>

3D Structure for #<Metabolite:0x00007fa4a3a0df08>