garamicidin D (CED0000060)

Record Information

Version

1.0

Creation Date

2016-06-03 13:32:13 UTC

Update Date

2026-09-01 14:29:19 UTC

Accession Number

CHEM045634

Identification

Common Name

garamicidin D

Class

Small Molecule

Description

garamicidin D belongs to the amino acids, peptides, and analogues, a subclass of carboxylic acids and derivatives within the organic compounds. With an average molecular weight of 1,882 g/mol, garamicidin D is a heavy molecule. Its chemical formula is C99H140N20O17. This compound is found in or released from six recorded sources, including throat preparations within healthcare, pharmaceuticals, and veterinary products, and the preparation of vinegar in food, food processing, and cookware. It is also associated with soap dispensers in household cleaning and consumer products, ceilings in building and construction, and antennas and electric hearing aids in electrical and electronic equipment. Recorded exposure routes for the substance include topical, nasal, auricular, and ophthalmic pathways. Regarding its biological activity, garamicidin D has one recorded protein target, acting as a binder of Dihydropteroate synthase (folP).

Contaminant Type

Not Available

Chemical Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Gramicidin J	MeSH
Linear gramicidin	MeSH
Gramicidin, linear	MeSH
Gramicidin a(1)	MeSH
Gramicidin D	MeSH
Gramicidins	MeSH
Gramicidin C	MeSH
Gramicidin p	MeSH
Gramicidin K	MeSH
Gramicidin dubos	MeSH
Gramicidin	MeSH
Gramicidin S	MeSH
Gramicidin b	MeSH
Gramoderm	MeSH
Gramicidin NF	MeSH
Gramicidin a	MeSH

Chemical Formula

C₉₉H₁₄₀N₂₀O₁₇

Average Molecular Mass

1882.332 g/mol

Monoisotopic Mass

1881.071 g/mol

CAS Registry Number

1405-97-6

IUPAC Name

(2R)-2-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2S)-1-hydroxy-2-{[(2S)-1-hydroxy-2-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2S)-1-hydroxy-2-{[(2R)-1-hydroxy-2-{[(2S)-1-hydroxy-2-[(1-hydroxy-2-{[(2S)-1-hydroxy-2-[(hydroxymethylidene)amino]-3-methylbutylidene]amino}ethylidene)amino]propylidene]amino}-4-methylpentylidene]amino}propylidene]amino}-3-methylbutylidene]amino}-3-methylbutylidene]amino}-3-methylbutylidene]amino}-3-(1H-indol-3-yl)propylidene]amino}-4-methylpentylidene]amino}-3-(1H-indol-3-yl)propylidene]amino}-4-methylpentylidene]amino}-3-(1H-indol-3-yl)propylidene]amino}-N-[(1S)-1-[(2-hydroxyethyl)-C-hydroxycarbonimidoyl]-2-(1H-indol-3-yl)ethyl]-4-methylpentanimidic acid

Traditional Name

SMILES

[H][C@@](C)(N=C(O)CN=C(O)[C@@]([H])(N=CO)C(C)C)C(O)=N[C@]([H])(CC(C)C)C(O)=N[C@@]([H])(C)C(O)=N[C@]([H])(C(C)C)C(O)=N[C@@]([H])(C(C)C)C(O)=N[C@@]([H])(C(C)C)C(O)=N[C@@]([H])(CC1=CNC2=CC=CC=C12)C(O)=N[C@]([H])(CC(C)C)C(O)=N[C@@]([H])(CC1=CNC2=CC=CC=C12)C(O)=N[C@]([H])(CC(C)C)C(O)=N[C@@]([H])(CC1=CNC2=CC=CC=C12)C(O)=N[C@]([H])(CC(C)C)C(O)=N[C@@]([H])(CC1=CNC2=CC=CC=C12)C(O)=NCCO

InChI Identifier

InChI=1S/C99H140N20O17/c1-51(2)37-73(109-86(123)59(17)107-81(122)49-105-96(133)82(55(9)10)106-50-121)89(126)108-60(18)87(124)117-84(57(13)14)98(135)119-85(58(15)16)99(136)118-83(56(11)12)97(134)116-80(44-64-48-104-72-34-26-22-30-68(64)72)95(132)112-76(40-54(7)8)92(129)115-79(43-63-47-103-71-33-25-21-29-67(63)71)94(131)111-75(39-53(5)6)91(128)114-78(42-62-46-102-70-32-24-20-28-66(62)70)93(130)110-74(38-52(3)4)90(127)113-77(88(125)100-35-36-120)41-61-45-101-69-31-23-19-27-65(61)69/h19-34,45-48,50-60,73-80,82-85,101-104,120H,35-44,49H2,1-18H3,(H,100,125)(H,105,133)(H,106,121)(H,107,122)(H,108,126)(H,109,123)(H,110,130)(H,111,131)(H,112,132)(H,113,127)(H,114,128)(H,115,129)(H,116,134)(H,117,124)(H,118,136)(H,119,135)/t59-,60-,73+,74+,75+,76+,77-,78-,79-,80-,82-,83-,84+,85-/m0/s1

InChI Key

ZWCXYZRRTRDGQE-SORVKSEFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as peptides. Peptides are compounds containing an amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Peptides

Alternative Parents

Substituents

Alpha peptide
3-alkylindole
Indole
Indole or derivatives
Substituted pyrrole
Benzenoid
Heteroaromatic compound
Pyrrole
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Alkanolamine
Azacycle
Carboximidic acid
Carboximidic acid derivative
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Primary alcohol
Alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Biological Properties

Status

Detected and Not Quantified

Origin

Not Available

Cellular Locations

Not Available

Biofluid Locations

Not Available

Tissue Locations

Not Available

Applications

Not Available

Biological Roles

Not Available

Chemical Roles

Not Available

Organoleptic Effects

Not Available

Physical Properties

State

Not Available

Appearance

Not Available

Experimental Properties

Property	Value
Melting Point	Not Available
Boiling Point	Not Available
Solubility	Not Available

Predicted Properties

Property	Value	Source
Water Solubility	0.012 g/L	ALOGPS
logP	4.28	ALOGPS
logP	18.54	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	2.95	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	33	ChemAxon
Hydrogen Donor Count	21	ChemAxon
Polar Surface Area	604.83 Å²	ChemAxon
Rotatable Bond Count	52	ChemAxon
Refractivity	517.98 m³·mol⁻¹	ChemAxon
Polarizability	206.8 Å³	ChemAxon
Number of Rings	8	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

Toxicity Profile

Mechanism of Toxicity

Not Available

Carcinogenicity (IARC Classification)

Not Available

Minimum Risk Level

Not Available

Symptoms

Not Available

Treatment

Not Available

Toxicity Values

Not Available

Health Effects

Health Effect	Relationship	Direction	Reference

Exposure Sources

Source ID	Source	Sector	Reference
390	Throat preparations	Healthcare, pharmaceuticals & veterinary products	Not Available
495	Ceilings	Building & Construction	Not Available
506	Antennas	Electrical & Electronic Equipment	Not Available
516	Electric Hearing Aids	Electrical & Electronic Equipment	Not Available
548	Preparation Of Vinegar	Food, food processing & cookware	Not Available
564	Soap Dispensers	Household cleaning & consumer products	Not Available
631	Anthraquinone Dyes	Textiles, leather & furnishings	Not Available
634	Buckles	Textiles, leather & furnishings	Not Available
640	Embroidering And Tufting	Textiles, leather & furnishings	Not Available
647	Multicolour Dyeing	Textiles, leather & furnishings	Not Available
651	Purses Money Bags Wallets	Textiles, leather & furnishings	Not Available
655	Slide Fasteners	Textiles, leather & furnishings	Not Available

Pathways

1 pathway

Gramicidin D Drug Metabolism Action Pathway

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Neutrophil collagenase	P22894	Humans	Predicted (SEA)	429.027
Click to view 3D structure	Melanocortin receptor 5	P41149	Mus musculus	Predicted (SEA)	224.284
Click to view 3D structure	Matrix metalloproteinase-9	P14780	Humans	Predicted (SEA)	627.776
Click to view 3D structure	Interstitial collagenase	P03956	Humans	Predicted (SEA)	505.008
Click to view 3D structure	Interleukin-1 receptor antagonist protein	P18510	Humans	Predicted (SEA)	105.641
Click to view 3D structure	Endoplasmic reticulum aminopeptidase 1	Q9NZ08	Humans	Predicted (SEA)	105.719
Click to view 3D structure	Melanocortin receptor 4	P56450	Mus musculus	Predicted (SEA)	245.147
Click to view 3D structure	Endoplasmic reticulum aminopeptidase 2	Q6P179	Humans	Predicted (SEA)	146.668
Click to view 3D structure	Endothiapepsin	P11838	Cryphonectria parasitica	Predicted (SEA)	47.7216
Click to view 3D structure	Endothelin receptor type B	P21451	Rattus norvegicus	Predicted (SEA)	152.04
Click to view 3D structure	Matrix metalloproteinase-14	P50281	Humans	Predicted (SEA)	515.128
Click to view 3D structure	5-hydroxytryptamine receptor 1A	P08908	Humans	Predicted (SEA)	1596.3
Click to view 3D structure	5-hydroxytryptamine receptor 2A	P28223	Humans	Predicted (SEA)	1779.32
Click to view 3D structure	Melanocortin receptor 4	P32245	Humans	Predicted (SEA)	307.037
Click to view 3D structure	Endothelin-1 receptor	P25101	Humans	Predicted (SEA)	202.875
Click to view 3D structure	Neuromedin-B receptor	P28336	Humans	Predicted (SEA)	176.64
Click to view 3D structure	5-hydroxytryptamine receptor 2C	P28335	Humans	Predicted (SEA)	1713.23
Click to view 3D structure	Melanocyte-stimulating hormone receptor	Q01727	Mus musculus	Predicted (SEA)	255.501
Click to view 3D structure	Substance-P receptor	P25103	Humans	Predicted (SEA)	599.05
Click to view 3D structure	5-hydroxytryptamine receptor 2B	P41595	Humans	Predicted (SEA)	1708.48
Click to view 3D structure	5-hydroxytryptamine receptor 6	P50406	Humans	Predicted (SEA)	1340.95
Click to view 3D structure	Melanocyte-stimulating hormone receptor	Q01726	Humans	Predicted (SEA)	273.251
Click to view 3D structure	Melanocortin receptor 3	P41968	Humans	Predicted (SEA)	288.12
Click to view 3D structure	Endothelin-converting enzyme 1	P42891	Bos taurus	Predicted (SEA)	52.8596
Click to view 3D structure	72 kDa type IV collagenase	P08253	Humans	Predicted (SEA)	621.626