4XYC

NANOMOLAR INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE 1: SYNTHESIS, BIOLOGICAL EVALUATION AND X-RAY CRYSTALLOGRAPHIC STUDIES

PDB DOI: https://doi.org/10.2210/pdb4XYC/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-02 Released: 2015-03-25
Deposition Author(s): Couturier, C., Silve, S., Morales, R., Ppessegue, B., Llopart, S., Nair, A., Bauer, A., Scheiper, B., poeverlein, c., Ganzhorn, A., Lagrange, S., Bacque, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.265
R-Value Work: 0.200
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Nanomolar inhibitors of Mycobacterium tuberculosis glutamine synthetase 1: Synthesis, biological evaluation and X-ray crystallographic studies.

Couturier, C., Silve, S., Morales, R., Pessegue, B., Llopart, S., Nair, A., Bauer, A., Scheiper, B., Poverlein, C., Ganzhorn, A., Lagrange, S., Bacque, E.

(2015) Bioorg Med Chem Lett 25: 1455-1459

PubMed: 25770781 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2015.02.035
Primary Citation of Related Structures:
4XYC

PubMed Abstract:
A series of imidazo[1,2-a]indeno[1,2-e]pyrazin-4-ones that potently inhibit M. tuberculosis glutamine synthetase (GlnA1) has been identified by high throughput screening. Exploration of this series was performed owing to a short chemistry program. Despite possibly nanomolar inhibitions, none of these compounds was active on whole cell Mtb, suggesting that GlnA1 may not be a suitable target to find new anti-tubercular drugs.

Organizational Affiliation

Sanofi R&D, TSU Infectious Disease, 195, route d'Espagne BP 13669, 31036 Toulouse Cedex 1, France. Electronic address: cedric.couturier@sanofi.com.

Macromolecule Content

Total Structure Weight: 1,294.2 kDa
Atom Count: 88,848
Modelled Residue Count: 11,144
Deposited Residue Count: 11,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	478	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: glnA1, glnA, MT2278 EC: 6.3.1.2
UniProt
Find proteins for P9WN38 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore P9WN38 Go to UniProtKB: P9WN38
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WN38
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2K9 Query on 2K9 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain MA [auth O] SDF format, chain VA [auth X] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth J] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain KA [auth M] SDF format, chain LA [auth N] SDF format, chain NA [auth P] SDF format, chain OA [auth Q] SDF format, chain PA [auth R] SDF format, chain QA [auth S] SDF format, chain RA [auth T] SDF format, chain SA [auth U] SDF format, chain TA [auth V] SDF format, chain UA [auth W] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain MA [auth O] MOL2 format, chain VA [auth X] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain LA [auth N] MOL2 format, chain NA [auth P] MOL2 format, chain OA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain QA [auth S] MOL2 format, chain RA [auth T] MOL2 format, chain SA [auth U] MOL2 format, chain TA [auth V] MOL2 format, chain UA [auth W] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], GA [auth I], HA [auth J], IA [auth K], JA [auth L], KA [auth M], LA [auth N], MA [auth O], NA [auth P], OA [auth Q], PA [auth R], QA [auth S], RA [auth T], SA [auth U], TA [auth V], UA [auth W], VA [auth X], Y [auth A], Z [auth B]	9-phenyl-4H-imidazo[1,2-a]indeno[1,2-e]pyrazin-4-one C₁₉ H₁₁ N₃ O SFZNDQGUHVYHPD-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth J] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth P] Focus chain OA [auth Q] Focus chain PA [auth R] Focus chain QA [auth S] Focus chain RA [auth T] Focus chain SA [auth U] Focus chain TA [auth V] Focus chain UA [auth W] Focus chain VA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.265
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 260.112	α = 90
b = 273.497	β = 90
c = 207.634	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2015-04-01
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description