6Y2J | pdb_00006y2j

Crystal structure of M. tuberculosis KasA in complex with 4,4,4-trifluoro-N-(isoquinolin-6-yl)butane-1-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb6Y2J/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: 2.89 Å
R-Value Free:
0.166 (Depositor), 0.168 (DCC)
R-Value Work:
0.116 (Depositor), 0.125 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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 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: 367.49 kDa
Atom Count: 25,455
Modeled Residue Count: 3,319
Deposited Residue Count: 3,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH]	435	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: kasA, Rv2245, MTCY427.26 EC: 2.3.1.41 (PDB Primary Data), 2.3.1.293 (UniProt)
UniProt
Find proteins for P9WQD9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQD9 Go to UniProtKB: P9WQD9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WQD9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O6W (Subject of Investigation/LOI) Query on O6W Download:Ideal Coordinates CCD File SDF format, chain CA [auth GGG] SDF format, chain FA [auth HHH] SDF format, chain K [auth AAA] SDF format, chain Q [auth CCC] SDF format, chain T [auth DDD] SDF format, chain W [auth EEE] SDF format, chain Z [auth FFF] SDF format, chain N [auth BBB] MOL2 format, chain CA [auth GGG] MOL2 format, chain FA [auth HHH] MOL2 format, chain K [auth AAA] MOL2 format, chain Q [auth CCC] MOL2 format, chain T [auth DDD] MOL2 format, chain W [auth EEE] MOL2 format, chain Z [auth FFF] MOL2 format, chain N [auth BBB] mmCIF format, chain CA [auth GGG] mmCIF format, chain FA [auth HHH] mmCIF format, chain K [auth AAA] mmCIF format, chain Q [auth CCC] mmCIF format, chain T [auth DDD] mmCIF format, chain W [auth EEE] mmCIF format, chain Z [auth FFF] mmCIF format, chain N [auth BBB]	CA [auth GGG] FA [auth HHH] K [auth AAA] N [auth BBB] Q [auth CCC] CA [auth GGG], FA [auth HHH], K [auth AAA], N [auth BBB], Q [auth CCC], T [auth DDD], W [auth EEE], Z [auth FFF]	4,4,4-tris(fluoranyl)-~{N}-isoquinolin-6-yl-butane-1-sulfonamide C₁₃ H₁₃ F₃ N₂ O₂ S MPUJMWAAXOTDHM-UHFFFAOYSA-N		Interactions Focus chain CA [auth GGG] Focus chain FA [auth HHH] Focus chain K [auth AAA] Focus chain N [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD] Focus chain W [auth EEE] Focus chain Z [auth FFF] Interactions & Density Focus chain CA [auth GGG] Focus chain FA [auth HHH] Focus chain K [auth AAA] Focus chain N [auth BBB] Focus chain Q [auth CCC] Focus chain T [auth DDD] Focus chain W [auth EEE] Focus chain Z [auth FFF]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth GGG] SDF format, chain DA [auth HHH] SDF format, chain I [auth AAA] SDF format, chain L [auth BBB] SDF format, chain U [auth EEE] SDF format, chain X [auth FFF] SDF format, chain R [auth DDD] SDF format, chain O [auth CCC] MOL2 format, chain AA [auth GGG] MOL2 format, chain DA [auth HHH] MOL2 format, chain I [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain U [auth EEE] MOL2 format, chain X [auth FFF] MOL2 format, chain R [auth DDD] MOL2 format, chain O [auth CCC] mmCIF format, chain AA [auth GGG] mmCIF format, chain DA [auth HHH] mmCIF format, chain I [auth AAA] mmCIF format, chain L [auth BBB] mmCIF format, chain U [auth EEE] mmCIF format, chain X [auth FFF] mmCIF format, chain R [auth DDD] mmCIF format, chain O [auth CCC]	AA [auth GGG] DA [auth HHH] I [auth AAA] L [auth BBB] O [auth CCC] AA [auth GGG], DA [auth HHH], I [auth AAA], L [auth BBB], O [auth CCC], R [auth DDD], U [auth EEE], X [auth FFF]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth GGG] Focus chain DA [auth HHH] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain O [auth CCC] Focus chain R [auth DDD] Focus chain U [auth EEE] Focus chain X [auth FFF] Interactions & Density Focus chain AA [auth GGG] Focus chain DA [auth HHH] Focus chain I [auth AAA] Focus chain L [auth BBB] Focus chain O [auth CCC] Focus chain R [auth DDD] Focus chain U [auth EEE] Focus chain X [auth FFF]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth GGG] SDF format, chain EA [auth HHH] SDF format, chain J [auth AAA] SDF format, chain P [auth CCC] SDF format, chain Y [auth FFF] SDF format, chain V [auth EEE] SDF format, chain S [auth DDD] SDF format, chain M [auth BBB] MOL2 format, chain BA [auth GGG] MOL2 format, chain EA [auth HHH] MOL2 format, chain J [auth AAA] MOL2 format, chain P [auth CCC] MOL2 format, chain Y [auth FFF] MOL2 format, chain V [auth EEE] MOL2 format, chain S [auth DDD] MOL2 format, chain M [auth BBB] mmCIF format, chain BA [auth GGG] mmCIF format, chain EA [auth HHH] mmCIF format, chain J [auth AAA] mmCIF format, chain P [auth CCC] mmCIF format, chain Y [auth FFF] mmCIF format, chain V [auth EEE] mmCIF format, chain S [auth DDD] mmCIF format, chain M [auth BBB]	BA [auth GGG] EA [auth HHH] J [auth AAA] M [auth BBB] P [auth CCC] BA [auth GGG], EA [auth HHH], J [auth AAA], M [auth BBB], P [auth CCC], S [auth DDD], V [auth EEE], Y [auth FFF]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth GGG] Focus chain EA [auth HHH] Focus chain J [auth AAA] Focus chain M [auth BBB] Focus chain P [auth CCC] Focus chain S [auth DDD] Focus chain V [auth EEE] Focus chain Y [auth FFF] Interactions & Density Focus chain BA [auth GGG] Focus chain EA [auth HHH] Focus chain J [auth AAA] Focus chain M [auth BBB] Focus chain P [auth CCC] Focus chain S [auth DDD] Focus chain V [auth EEE] Focus chain Y [auth FFF]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.89 Å
R-Value Free: 0.166 (Depositor), 0.168 (DCC)
R-Value Work: 0.116 (Depositor), 0.125 (DCC)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.242	α = 90
b = 151.242	β = 90
c = 147.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Chung, C.

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2020-05-20
Changes: Database references
Version 1.2: 2024-05-15
Changes: Data collection, Database references, Derived calculations