Daptomycin (CED0002286)

Record Information

Version

1.0

Creation Date

2016-06-03 11:54:08 UTC

Update Date

2026-05-14 16:23:58 UTC

Accession Number

CHEM044231

Identification

Common Name

Daptomycin

Class

Small Molecule

Description

Daptomycin is an organic compound with the chemical formula C72H101N17O26. Daptomycin belongs to the depsipeptides, a subclass of peptidomimetics within the organic compounds. With an average molecular weight of 1,621 g/mol, Daptomycin is a heavy molecule. This compound is recorded as being found in or released from three sources: antennas in electrical and electronic equipment, and antibacterials and antibiotics within healthcare, pharmaceuticals, and veterinary products. Recorded exposure routes for Daptomycin include oral, intravenous, and inhalation. In terms of biological activity, Daptomycin 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
Deptomycin	MeSH
Daptomycin, 9-L beta-aspartic acid	MeSH
Cubicin	MeSH
Daptomycin, 9 L beta aspartic acid	MeSH

Chemical Formula

C₇₂H₁₀₁N₁₇O₂₆

Average Molecular Mass

1620.693 g/mol

Monoisotopic Mass

1619.710 g/mol

CAS Registry Number

103060-53-3

IUPAC Name

(3S)-3-{[(3S,6S,9R,15S,18R,21S,24S)-3-[2-(2-aminophenyl)-2-oxoethyl]-24-(3-aminopropyl)-15,21-bis(carboxymethyl)-6-(1-carboxypropan-2-yl)-5,8,11,14,17,20,23,26,29-nonahydroxy-9-(hydroxymethyl)-18,31-dimethyl-2-oxo-1-oxa-4,7,10,13,16,19,22,25,28-nonaazacyclohentriaconta-4,7,10,13,16,19,22,25,28-nonaen-30-yl]-C-hydroxycarbonimidoyl}-3-{[(2S)-1-hydroxy-2-{[(2S)-1-hydroxy-2-[(1-hydroxydecylidene)amino]-3-(1H-indol-3-yl)propylidene]amino}-3-(C-hydroxycarbonimidoyl)propylidene]amino}propanoic acid

Traditional Name

SMILES

[H]C(C)(CC(O)=O)[C@]1([H])N=C(O)[C@@]([H])(CO)N=C(O)CN=C(O)[C@]([H])(CC(O)=O)N=C(O)[C@@]([H])(C)N=C(O)[C@]([H])(CC(O)=O)N=C(O)[C@]([H])(CCCN)N=C(O)CN=C(O)C([H])(N=C(O)[C@]([H])(CC(O)=O)N=C(O)[C@]([H])(CC(O)=N)N=C(O)[C@]([H])(CC2=CNC3=CC=CC=C23)N=C(O)CCCCCCCCC)C([H])(C)OC(=O)[C@]([H])(CC(=O)C2=CC=CC=C2N)N=C1O

InChI Identifier

InChI=1S/C72H101N17O26/c1-5-6-7-8-9-10-11-22-53(93)81-44(25-38-31-76-42-20-15-13-17-39(38)42)66(108)84-45(27-52(75)92)67(109)86-48(30-59(102)103)68(110)89-61-37(4)115-72(114)49(26-51(91)40-18-12-14-19-41(40)74)87-71(113)60(35(2)24-56(96)97)88-69(111)50(34-90)82-55(95)32-77-63(105)46(28-57(98)99)83-62(104)36(3)79-65(107)47(29-58(100)101)85-64(106)43(21-16-23-73)80-54(94)33-78-70(61)112/h12-15,17-20,31,35-37,43-50,60-61,76,90H,5-11,16,21-30,32-34,73-74H2,1-4H3,(H2,75,92)(H,77,105)(H,78,112)(H,79,107)(H,80,94)(H,81,93)(H,82,95)(H,83,104)(H,84,108)(H,85,106)(H,86,109)(H,87,113)(H,88,111)(H,89,110)(H,96,97)(H,98,99)(H,100,101)(H,102,103)/t35?,36-,37?,43+,44+,45+,46+,47+,48+,49+,50-,60+,61?/m1/s1

InChI Key

DOAKLVKFURWEDJ-OFNKPWESSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as primary carboxylic acid amides. Primary carboxylic acid amides are compounds comprising primary carboxylic acid amide functional group, with the general structure RC(=O)NH2.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Carboxylic acid derivatives

Direct Parent

Primary carboxylic acid amides

Alternative Parents

Substituents

Primary carboxylic acid amide
Alkyl chloride
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Organoiodide
Organochloride
Organohalogen compound
Carbonyl group
Alkyl iodide
Alkyl halide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Halogenated fatty acids (LMFA01090147 )

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	0.046 g/L	ALOGPS
logP	0.93	ALOGPS
logP	4.69	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	2.38	ChemAxon
Physiological Charge	-7	ChemAxon
Hydrogen Acceptor Count	41	ChemAxon
Hydrogen Donor Count	23	ChemAxon
Polar Surface Area	748.38 Å²	ChemAxon
Rotatable Bond Count	35	ChemAxon
Refractivity	411.28 m³·mol⁻¹	ChemAxon
Polarizability	159.74 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0uei-0000195000-d307278a65d07c4ef2b0	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0itc-2612291000-e40ed1a6d6520710f0d5	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-03mi-5914111000-d12a04754b89ad30031c	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0fk9-0000094000-82873a0f8cc1583d67ca	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0ukc-1100194000-19118807733955c744b4	Not Available	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum	splash10-0597-9622320000-d6bf995b65794136005f	Not Available	View Spectrum

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
306	Antibiotics	Healthcare, pharmaceuticals & veterinary products	Not Available
347	Antibacterials	Healthcare, pharmaceuticals & veterinary products	Not Available
506	Antennas	Electrical & Electronic Equipment	Not Available

Pathways

1 pathway

Daptomycin Drug Metabolism Action Pathway

Targets

Structure	Protein	UniProt ID	Organism	Relationship	Details
Click to view 3D structure	Gastric inhibitory polypeptide receptor	Q0P543	Mus musculus	Predicted (SEA)	116.93
Click to view 3D structure	Glucagon-like peptide 1 receptor	P43220	Humans	Predicted (SEA)	290.767
Click to view 3D structure	Glucagon-like peptide 1 receptor	O35659	Mus musculus	Predicted (SEA)	148.458
Click to view 3D structure	Delta-type opioid receptor	P41143	Humans	Predicted (SEA)	1520.47
Click to view 3D structure	Gastrin/cholecystokinin type B receptor	P32239	Humans	Predicted (SEA)	383.563
Click to view 3D structure	Glucagon-like peptide 2 receptor	Q9Z0W0	Rattus norvegicus	Predicted (SEA)	144.8
Click to view 3D structure	Glucagon receptor	P47871	Humans	Predicted (SEA)	305.247
Click to view 3D structure	Cholecystokinin receptor type A	P32238	Humans	Predicted (SEA)	301.199
Click to view 3D structure	Delta-type opioid receptor	P32300	Mus musculus	Predicted (SEA)	574.294
Click to view 3D structure	Mu-type opioid receptor	P33535	Rattus norvegicus	Predicted (SEA)	821.154
Click to view 3D structure	Glucagon receptor	Q61606	Mus musculus	Predicted (SEA)	165.585
Click to view 3D structure	Glucagon-like peptide 2 receptor	O95838	Humans	Predicted (SEA)	151.261
Click to view 3D structure	Segment polarity protein dishevelled homolog DVL-2	O14641	Humans	Predicted (SEA)	184.347
Click to view 3D structure	Mu-type opioid receptor	P97266	Cavia porcellus	Predicted (SEA)	726.8
Click to view 3D structure	Thiol:disulfide interchange protein DsbA	P0AEG4	Escherichia coli (strain K12)	Predicted (SEA)	181.467
Click to view 3D structure	Tumor necrosis factor receptor superfamily member 10B	O14763	Humans	Predicted (SEA)	138.027
Click to view 3D structure	Endothelin receptor type B	Q9N0W7	Oryctolagus cuniculus	Predicted (SEA)	123.858
Click to view 3D structure	Glucagon-like peptide 1 receptor	F8V479	Macaca fascicularis	Predicted (SEA)	143.865
Click to view 3D structure	Glucagon receptor	P30082	Rattus norvegicus	Predicted (SEA)	208.247
Click to view 3D structure	Gastric inhibitory polypeptide receptor	P48546	Humans	Predicted (SEA)	304.157
Click to view 3D structure	Alpha-cobratoxin	P01391	Naja kaouthia	Predicted (SEA)	168.933
Click to view 3D structure	Envelope glycoprotein gp160	Q72502	Human immunodeficiency virus 1	Predicted (SEA)	129.152
Click to view 3D structure	Somatostatin receptor type 5	P35346	Humans	Predicted (SEA)	519.021
Click to view 3D structure	Somatostatin receptor type 3	P32745	Humans	Predicted (SEA)	470.209
Click to view 3D structure	Somatostatin receptor type 4	P31391	Humans	Predicted (SEA)	381.383