ChemFOnt: Showing chemical card for Desmosine (CFc000000446)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:44:50 UTC

Chemfont ID

CFc000000446

Molecule Identification

Common Name

Desmosine

Definition

Desmosine is formed by condensation of four molecules of lysine into a pyridinium ring. Elastin molecules aggregate in the extracellular space where they are crosslinked by stable desmosine bridges. The resulting polymer is structurally organized as branched fibers and lamellae, which, in skin, are wider (a few microns) in the deep dermis and become progressively thinner (fraction of a micron) towards the papillary dermis. Several general and local factors seem to regulate elastin gene expression, deposition and degradation. (PMID: 9297692 ). Desmosines are crosslinking amino acids unique to mature elastin in humans. Owing to this unicity, they have been discussed as potentially indicators of connective tissue disorders whose clinical manifestations are mostly the result of elastin degradation. (PMID: 17390614 ). Emphysema (Pulmonary emphysema is a devastating disease for which there is no effective treatment) is associated with degradation of elastic fibers (PMID: 14704646 ). It has been shown that the urinary concentration of elastin specific crosslinks, desmosine correlates well with liver fibrosis score in biopsy specimens from patients with liver disease secondary to hepatitis C virus and alcohol. (PMID: 10996125 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
4-(4-amino-4-Carboxybutyl)-1-(5-amino-5-carboxypentyl)-3,5-bis(3-amino-3-carboxypropyl)pyridinium	MeSH

Chemical Formula

C₂₄H₄₀N₅O₈

Average Molecular Weight

526.6031

Monoisotopic Molecular Weight

526.287688281

IUPAC Name

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

Traditional Name

desmosine

CAS Registry Number

11003-57-9

SMILES

NC(CCCC[N+]1=CC(CCC(N)C(O)=O)=C(CCCC(N)C(O)=O)C(CCC(N)C(O)=O)=C1)C(O)=O

InChI Identifier

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

InChI Key

VEVRNHHLCPGNDU-UHFFFAOYSA-O

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
Amino acid
Azacycle
Organoheterocyclic compound
Carboxylic acid
Organic nitrogen compound
Organic oxygen compound
Organic oxide
Organopnictogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Hydrocarbon derivative
Amine
Organic cation
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Kidney (HMDB: HMDB0000572)

Tissue

Epithelium

Epidermis (HMDB: HMDB0000572)

Excreta

Biofluid or Excreta

Urine (PMID: 14563926)

Cellular substructure

Cytoplasm (HMDB: HMDB0000572)

Source

Endogenous

Endogenous (HMDB: HMDB0000572)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Not Available

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	0.012 g/L	ALOGPS
logP	-4.5	ALOGPS
logP	-13	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	8	ChemAxon
Polar Surface Area	257.16 Å²	ChemAxon
Rotatable Bond Count	19	ChemAxon
Refractivity	133.53 m³·mol⁻¹	ChemAxon
Polarizability	56.68 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

FooDB ID

FDB000516

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Desmosine

METLIN ID

Not Available

PubChem Compound

25435

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Rencher, William Franklin, Jr. Design and synthesis of desmosine-like peptidyl carbamates as novel inhibitors of human leukocyte elastase. (1988), 164 pp. CAN 111:233627 AN 1989:633627

Showing chemical card for Desmosine (CFc000000446)

MOL for CFc000000446 (Desmosine)

3D MOL for CFc000000446 (Desmosine)

3D SDF for CFc000000446 (Desmosine)

3D-SDF for CFc000000446 (Desmosine)

PDB for CFc000000446 (Desmosine)

3D PDB for CFc000000446 (Desmosine)

SMILES for CFc000000446 (Desmosine)

INCHI for CFc000000446 (Desmosine)

Structure for CFc000000446 (Desmosine)

3D Structure for CFc000000446 (Desmosine)