3ZXR

Crystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with tri-substituted imidazole inhibitor (3-(2-tert-butyl- 5-(pyridin-4-yl)-1H-imidazol-4-yl)quinoline) and L-methionine-S- sulfoximine phosphate.

PDB DOI: https://doi.org/10.2210/pdb3ZXR/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-15 Released: 2012-04-04
Deposition Author(s): Nilsson, M.T., Mowbray, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.245
R-Value Work: 0.225
R-Value Observed: 0.226

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Trisubstituted Imidazoles as Mycobacterium Tuberculosis Glutamine Synthetase Inhibitors.

Gising, J., Nilsson, M.T., Odell, L.R., Yahiaoui, S., Lindh, M., Iyer, H., Sinha, A.M., Srinivasa, B.R., Larhed, M., Mowbray, S.L., Karlen, A.

(2012) J Med Chem 55: 2894

PubMed: 22369127 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm201212h
Primary Citation of Related Structures:
3ZXR, 3ZXV

PubMed Abstract:
Mycobacterium tuberculosis glutamine synthetase (MtGS) is a promising target for antituberculosis drug discovery. In a recent high-throughput screening study we identified several classes of MtGS inhibitors targeting the ATP-binding site. We now explore one of these classes, the 2-tert-butyl-4,5-diarylimidazoles, and present the design, synthesis, and X-ray crystallographic studies leading to the identification of MtGS inhibitors with submicromolar IC(50) values and promising antituberculosis MIC values.

Organizational Affiliation

Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, Box 574, SE-751 23 Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 332.26 kDa
Atom Count: 24,276
Modelled Residue Count: 2,850
Deposited Residue Count: 2,916
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMINE SYNTHETASE 1	A, B, C, D, E A, B, C, D, E, F	486	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 EC: 6.3.1.2
UniProt
Find proteins for P9WN39 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WN39 Go to UniProtKB: P9WN39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WN39
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IQ1 Query on IQ1 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain IA [auth E] SDF format, chain N [auth B] SDF format, chain PA [auth F] SDF format, chain U [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth B] MOL2 format, chain PA [auth F] MOL2 format, chain U [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain N [auth B] mmCIF format, chain PA [auth F] mmCIF format, chain U [auth C]	BA [auth D] G [auth A] IA [auth E] N [auth B] PA [auth F] BA [auth D], G [auth A], IA [auth E], N [auth B], PA [auth F], U [auth C]	3-(2-TERT-BUTYL-5-(PYRIDIN-4-YL)-1H-IMIDAZOL-4-YL)QUINOLINE C₂₁ H₂₀ N₄ WOMTUQORZZQBPJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain N [auth B] Focus chain PA [auth F] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain IA [auth E] Focus chain N [auth B] Focus chain PA [auth F] Focus chain U [auth C]
P3S Query on P3S Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain K [auth A] SDF format, chain MA [auth E] SDF format, chain R [auth B] SDF format, chain TA [auth F] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth F] mmCIF format, chain Y [auth C]	FA [auth D] K [auth A] MA [auth E] R [auth B] TA [auth F] FA [auth D], K [auth A], MA [auth E], R [auth B], TA [auth F], Y [auth C]	L-METHIONINE-S-SULFOXIMINE PHOSPHATE C₅ H₁₃ N₂ O₆ P S QQFOFBSCSWFFPB-NMAPHRJESA-N		Interactions Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain TA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain K [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain TA [auth F] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain L [auth A] SDF format, chain NA [auth E] SDF format, chain S [auth B] SDF format, chain UA [auth F] SDF format, chain Z [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain Z [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain Z [auth C]	GA [auth D] L [auth A] NA [auth E] S [auth B] UA [auth F] GA [auth D], L [auth A], NA [auth E], S [auth B], UA [auth F], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain GA [auth D] Focus chain L [auth A] Focus chain NA [auth E] Focus chain S [auth B] Focus chain UA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain GA [auth D] Focus chain L [auth A] Focus chain NA [auth E] Focus chain S [auth B] Focus chain UA [auth F] Focus chain Z [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain M [auth A] SDF format, chain OA [auth E] SDF format, chain T [auth B] SDF format, chain VA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain VA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain VA [auth F]	AA [auth C] HA [auth D] M [auth A] OA [auth E] T [auth B] AA [auth C], HA [auth D], M [auth A], OA [auth E], T [auth B], VA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain M [auth A] Focus chain OA [auth E] Focus chain T [auth B] Focus chain VA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain M [auth A] Focus chain OA [auth E] Focus chain T [auth B] Focus chain VA [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain SA [auth F] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain SA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain SA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	CA [auth D] DA [auth D] EA [auth D] H [auth A] I [auth A] CA [auth D], DA [auth D], EA [auth D], H [auth A], I [auth A], J [auth A], JA [auth E], KA [auth E], LA [auth E], O [auth B], P [auth B], Q [auth B], QA [auth F], RA [auth F], SA [auth F], V [auth C], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain SA [auth F] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
IQ1	PDBBind: 3ZXR	IC50: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.245
R-Value Work: 0.225
R-Value Observed: 0.226
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.26	α = 90
b = 227.47	β = 90
c = 200.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Nilsson, M.T.

Mowbray, S.L.

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2019-05-15
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description