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EBL-3647   Click here for help

GtoPdb Ligand ID: 14230

PDB Ligand
Compound class: Synthetic organic
Comment: EBL-3647 is from a series of antibacterial compounds that target UDP-2,3-diacylglucosamine hydrolase (LpxH), an essential enzyme in the lipopolysaccharide synthesis pathway, that is conserved in the majority of Gram-negative bacteria but absent in human [1]. EBL-3647 is a derivative of JEDI-1444 and was identified as part of a programme to develop LpxH inhibitors with activity against efflux-proficient Gram-negative bacteria.
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 14
Hydrogen bond donors 2
Rotatable bonds 11
Topological polar surface area 201.63
Molecular weight 667.81
XLogP -1.37
No. Lipinski's rules broken 2

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CC1=NC(=NC(=C1)C#N)N2CCN(CC2)S(=O)(=O)C3=CC=C(C=C3)NC(=O)C4=CC(=CC=C4N(C)S(=O)(=O)C)CN5CC(CN)C5
Isomeric SMILES O=S(N1CCN(CC1)C2=NC(C)=CC(C#N)=N2)(C3=CC=C(NC(C4=C(N(C)S(=O)(C)=O)C=CC(CN5CC(CN)C5)=C4)=O)C=C3)=O
InChI InChI=1S/C30H37N9O5S2/c1-21-14-25(17-32)35-30(33-21)38-10-12-39(13-11-38)46(43,44)26-7-5-24(6-8-26)34-29(40)27-15-22(18-37-19-23(16-31)20-37)4-9-28(27)36(2)45(3,41)42/h4-9,14-15,23H,10-13,16,18-20,31H2,1-3H3,(H,34,40)
InChI Key YZXAAZBUIFNWLC-UHFFFAOYSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
5-[[3-(aminomethyl)azetidin-1-yl]methyl]-N-[4-[4-(4-cyano-6-methylpyrimidin-2-yl)piperazin-1-yl]sulfonylphenyl]-2-[methyl(methylsulfonyl)amino]benzamide
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo EBL-3647
Other databases
CAS Registry No. 2851907-60-1 (source: Scifinder)
PubChem CID 171121778
RCSB PDB Ligand VN6
Search Google for chemical match using the InChIKey YZXAAZBUIFNWLC-UHFFFAOYSA-N
Search Google for chemicals with the same backbone YZXAAZBUIFNWLC
UniChem Compound Search for chemical match using the InChIKey YZXAAZBUIFNWLC-UHFFFAOYSA-N
UniChem Connectivity Search for chemical match using the InChIKey YZXAAZBUIFNWLC-UHFFFAOYSA-N