clovibactin   Click here for help

GtoPdb Ligand ID: 13080

Synonyms: Novo29
Compound class: Natural product or derivative
Comment: Clovibactin is a natural peptide isolated from the uncultured soil-dwelling bacterium Eleftheria terrae ssp. carolina [3]. It is related in structure to teixobactin and is active against Gram-positive bacteria [2]. The chemical structure is one of those claimed in patent WO2018187173 filed by NovoBiotic Pharmaceuticals [1]. It is in preclinical development as a potential treatment for a wide range of bacterial infections caused by Gram-positive pathogens.
Functionally, clovibactin disrupts bacterial cell wall synthesis by binding to the pyrophosphate of multiple essential peptidoglycan precursors (C55PP, lipid II, and lipid IIIWTA) [3].
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 21
Hydrogen bond donors 11
Rotatable bonds 26
Topological polar surface area 345.36
Molecular weight 903.08
XLogP 2.54
No. Lipinski's rules broken 4
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES CC(C)C[C@H]1C(=O)N[C@@H](CC(C)C)C(=O)O[C@H]([C@H](C(=O)N[C@@H](C)C(=O)N1)NC(=O)[C@H](CO)NC(=O)[C@@H](CCCCN)NC(=O)[C@@H](CC(C)C)NC(=O)[C@H](CC2=CC=CC=C2)N)C(=O)N
Isomeric SMILES C[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)O[C@H]([C@H](C(=O)N1)NC(=O)[C@H](CO)NC(=O)[C@@H](CCCCN)NC(=O)[C@@H](CC(C)C)NC(=O)[C@H](CC2=CC=CC=C2)N)C(=O)N)CC(C)C)CC(C)C
InChI InChI=1S/C43H70N10O11/c1-22(2)17-29-40(60)51-31(19-24(5)6)43(63)64-34(35(46)55)33(42(62)47-25(7)36(56)49-29)53-41(61)32(21-54)52-38(58)28(15-11-12-16-44)48-39(59)30(18-23(3)4)50-37(57)27(45)20-26-13-9-8-10-14-26/h8-10,13-14,22-25,27-34,54H,11-12,15-21,44-45H2,1-7H3,(H2,46,55)(H,47,62)(H,48,59)(H,49,56)(H,50,57)(H,51,60)(H,52,58)(H,53,61)/t25-,27-,28+,29-,30+,31-,32-,33+,34+/m0/s1
InChI Key SMQAHGKBWXPEHB-HHHSQLJLSA-N
References
1. Hughes D, Spoering A, Peoples AJ, Ling LL, Nitti A , Millett W, Zullo A, Lewis K, Epstein S, Desrosiers A et al.. (2018)
Novel depsipeptides and uses thereof.
Patent number: WO2018187173A1. Assignee: Novobiotic Pharmaceuticals, Llc. Priority date: 30/03/2018. Publication date: 11/10/2018.
2. Krumberger M, Li X, Kreutzer AG, Peoples AJ, Nitti AG, Cunningham AM, Jones CR, Achorn C, Ling LL, Hughes DE et al.. (2023)
Synthesis and Stereochemical Determination of the Peptide Antibiotic Novo29.
J Org Chem, 88 (4): 2214-2220. [PMID:36655882]
3. Shukla R, Peoples AJ, Ludwig KC, Maity S, Derks MGN, De Benedetti S, Krueger AM, Vermeulen BJA, Harbig T, Lavore F et al.. (2023)
An antibiotic from an uncultured bacterium binds to an immutable target.
Cell, 186 (19): 4059-4073.e27. [PMID:37611581]