6Y2I

Crystal structure of M. tuberculosis KasA in complex with N-(1H-indazol-5-yl)butane-1-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb6Y2I/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-02-16 Released: 2020-04-08
Deposition Author(s): Chung, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free: 0.136
R-Value Work: 0.122

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Exploring the SAR of the beta-Ketoacyl-ACP Synthase Inhibitor GSK3011724A and Optimization around a Genotoxic Metabolite.

Cunningham, F., Esquivias, J., Fernandez-Menendez, R., Perez, A., Guardia, A., Escribano, J., Rivero, C., Vimal, M., Cacho, M., de Dios-Anton, P., Martinez-Martinez, M.S., Jimenez, E., Huertas Valentin, L., Rebollo-Lopez, M.J., Lopez-Roman, E.M., Sousa-Morcuende, V., Rullas, J., Neu, M., Chung, C.W., Bates, R.H.

(2020) ACS Infect Dis 6: 1098-1109

PubMed: 32196311 Search on PubMed
DOI: https://doi.org/10.1021/acsinfecdis.9b00493
Primary Citation of Related Structures:
6Y2I, 6Y2J

PubMed Abstract:
In the course of optimizing a novel indazole sulfonamide series that inhibits β-ketoacyl-ACP synthase (KasA) of Mycobacterium tuberculosis , a mutagenic aniline metabolite was identified. Further lead optimization efforts were therefore dedicated to eliminating this critical liability by removing the embedded aniline moiety or modifying its steric or electronic environment. While the narrow SAR space against the target ultimately rendered this goal unsuccessful, key structural knowledge around the binding site of this underexplored target for TB was generated to inform future discovery efforts.

Organizational Affiliation

Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 92.36 kDa
Atom Count: 7,243
Modelled Residue Count: 826
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 1	A [auth AAA], B [auth BBB]	435	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: kasA, Rv2245, MTCY427.26 EC: 2.3.1.41
UniProt
Find proteins for P9WQD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQD9 Go to UniProtKB: P9WQD9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O6Z (Subject of Investigation/LOI) Query on O6Z Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain P [auth BBB] MOL2 format, chain H [auth AAA] MOL2 format, chain P [auth BBB]	H [auth AAA], P [auth BBB]	~{N}-(1~{H}-indazol-5-yl)butane-1-sulfonamide C₁₁ H₁₅ N₃ O₂ S OPXDHLZGQKADDC-UHFFFAOYSA-N		Interactions Focus chain H [auth AAA] Focus chain P [auth BBB] Interactions & Density Focus chain H [auth AAA] Focus chain P [auth BBB]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth AAA] SDF format, chain R [auth BBB] MOL2 format, chain J [auth AAA] MOL2 format, chain R [auth BBB]	J [auth AAA], R [auth BBB]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain R [auth BBB] Interactions & Density Focus chain J [auth AAA] Focus chain R [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain K [auth BBB] SDF format, chain O [auth BBB] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain K [auth BBB] MOL2 format, chain O [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB]	C [auth AAA] D [auth AAA] E [auth AAA] F [auth AAA] G [auth AAA] C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], K [auth BBB], L [auth BBB], M [auth BBB], N [auth BBB], O [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Focus chain O [auth BBB]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth AAA] SDF format, chain Q [auth BBB] MOL2 format, chain I [auth AAA] MOL2 format, chain Q [auth BBB]	I [auth AAA], Q [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth AAA] Focus chain Q [auth BBB] Interactions & Density Focus chain I [auth AAA] Focus chain Q [auth BBB]