NP-MRD: Showing NP-Card for Isodesmosine (NP0086495)

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Record Information

Version

2.0

Created at

2022-05-11 16:21:20 UTC

Updated at

2022-05-11 16:21:20 UTC

NP-MRD ID

NP0086495

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Isodesmosine

Description

Not Available

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241220262D          

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M  CHG  2   4   1  37  -1
M  END

     RDKit          3D

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M  CHG  2  25   1  34  -1
M  END


  Mrv0541 02241220262D          

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 13 31  1  0  0  0  0
 14 15  1  0  0  0  0
 14 30  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 34  1  0  0  0  0
 23 24  2  0  0  0  0
 23 35  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 33  1  0  0  0  0
 28 29  1  0  0  0  0
 28 32  2  0  0  0  0
M  CHG  2   4   1  37  -1
M  END
> <DATABASE_ID>
NP0086495

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCCC1=[N+](CCCCC(N)C([O-])=O)C=C(CCC(N)C(O)=O)C=C1CCC(N)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H39N5O8/c25-16(21(30)31)4-1-2-11-29-13-14(7-9-18(27)23(34)35)12-15(8-10-19(28)24(36)37)20(29)6-3-5-17(26)22(32)33/h12-13,16-19H,1-11,25-28H2,(H3-,30,31,32,33,34,35,36,37)

> <INCHI_KEY>
RGXCTRIQQODGIZ-UHFFFAOYSA-N

> <FORMULA>
C24H39N5O8

> <MOLECULAR_WEIGHT>
525.5952

> <EXACT_MASS>
525.279863249

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
56.24387981682703

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,5-bis(3-amino-3-carboxypropyl)-2-(4-amino-4-carboxybutyl)-1-(5-amino-5-carboxylatopentyl)pyridin-1-ium

> <ALOGPS_LOGP>
-4.24

> <JCHEM_LOGP>
-13.823956962703773

> <ALOGPS_LOGS>
-4.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
1.4817920282861223

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0397294744455632

> <JCHEM_PKA_STRONGEST_BASIC>
10.123567041622112

> <JCHEM_POLAR_SURFACE_AREA>
259.99

> <JCHEM_REFRACTIVITY>
144.1889

> <JCHEM_ROTATABLE_BOND_COUNT>
19

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.06e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,5-bis(3-amino-3-carboxypropyl)-2-(4-amino-4-carboxybutyl)-1-(5-amino-5-carboxylatopentyl)pyridin-1-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       1.924  -1.847   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.538  -2.617   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.692  -1.847   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      -0.692  -0.309   0.000  0.00  0.00           N+1
HETATM    5  C   UNK     0      -2.078   0.461   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.464  -0.309   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.464  -1.847   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.696  -2.617   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.696  -4.157   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.464  -4.927   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.078  -4.311   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.310   5.081   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.542   4.311   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.696   2.771   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.310   2.001   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.310   0.461   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.924  -0.309   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.538   0.461   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.538   2.001   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.692   2.771   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.692   4.311   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.078   5.081   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.464   4.311   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -3.464   2.771   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       0.692  -4.157   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.078  -4.927   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.310  -4.157   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.696  -5.081   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.082  -4.465   0.000  0.00  0.00           O+0
HETATM   30  N   UNK     0       5.928   2.001   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0       5.928   5.081   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.542  -6.621   0.000  0.00  0.00           O+0
HETATM   33  N   UNK     0       3.926  -2.771   0.000  0.00  0.00           N+0
HETATM   34  N   UNK     0      -2.078   6.621   0.000  0.00  0.00           N+0
HETATM   35  O   UNK     0      -4.696   5.081   0.000  0.00  0.00           O+0
HETATM   36  N   UNK     0      -6.082  -4.927   0.000  0.00  0.00           N+0
HETATM   37  O   UNK     0      -3.464  -6.467   0.000  0.00  0.00           O-1
CONECT    1    2   17                                                       
CONECT    2    1    3   25                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   18                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   36                                                  
CONECT   10    9   11   37                                                  
CONECT   11   10                                                            
CONECT   12   13                                                            
CONECT   13   12   14   31                                                  
CONECT   14   13   15   30                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17    1   16   18                                                  
CONECT   18    4   17   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24   35                                                  
CONECT   24   23                                                            
CONECT   25    2   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   33                                                  
CONECT   28   27   29   32                                                  
CONECT   29   28                                                            
CONECT   30   14                                                            
CONECT   31   13                                                            
CONECT   32   28                                                            
CONECT   33   27                                                            
CONECT   34   22                                                            
CONECT   35   23                                                            
CONECT   36    9                                                            
CONECT   37   10                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₉N₅O₈

Average Mass

525.5952 Da

Monoisotopic Mass

525.27986 Da

IUPAC Name

3,5-bis(3-amino-3-carboxypropyl)-2-(4-amino-4-carboxybutyl)-1-(5-amino-5-carboxylatopentyl)pyridin-1-ium

Traditional Name

3,5-bis(3-amino-3-carboxypropyl)-2-(4-amino-4-carboxybutyl)-1-(5-amino-5-carboxylatopentyl)pyridin-1-ium

CAS Registry Number

Not Available

SMILES

NC(CCCC1=[N+](CCCCC(N)C([O-])=O)C=C(CCC(N)C(O)=O)C=C1CCC(N)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C24H39N5O8/c25-16(21(30)31)4-1-2-11-29-13-14(7-9-18(27)23(34)35)12-15(8-10-19(28)24(36)37)20(29)6-3-5-17(26)22(32)33/h12-13,16-19H,1-11,25-28H2,(H3-,30,31,32,33,34,35,36,37)

InChI Key

RGXCTRIQQODGIZ-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetracarboxylic acids and derivatives. These are carboxylic acids containing exactly four carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tetracarboxylic acids and derivatives

Direct Parent

Tetracarboxylic acids and derivatives

Alternative Parents

Substituents

Tetracarboxylic acid or derivatives
Alpha-amino acid
Alpha-amino acid or derivatives
Aralkylamine
Pyridine
Pyridinium
Heteroaromatic compound
Amino acid or derivatives
Carboxylic acid salt
Amino acid
Azacycle
Organoheterocyclic compound
Carboxylic acid
Organic salt
Organic oxide
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Organic oxygen compound
Carbonyl group
Organic nitrogen compound
Organic zwitterion
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-4.2	ALOGPS
logP	-14	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	1.04	ChemAxon
pKa (Strongest Basic)	10.12	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	259.99 Å²	ChemAxon
Rotatable Bond Count	19	ChemAxon
Refractivity	144.19 m³·mol⁻¹	ChemAxon
Polarizability	56.24 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB000467

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Isodesmosine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Isodesmosine (NP0086495)

MOL for NP0086495 (Isodesmosine)

3D MOL for NP0086495 (Isodesmosine)

3D SDF for NP0086495 (Isodesmosine)

3D-SDF for NP0086495 (Isodesmosine)

PDB for NP0086495 (Isodesmosine)

3D PDB for NP0086495 (Isodesmosine)

SMILES for NP0086495 (Isodesmosine)

INCHI for NP0086495 (Isodesmosine)

Structure for NP0086495 (Isodesmosine)

3D Structure for NP0086495 (Isodesmosine)