5OIS | pdb_00005ois

InhA (T2A mutant) complexed with 4-((5-Amino-3-methyl-1H-pyrazol-1-yl)methyl)-N-(2-chloro-4-fluorobenzyl)benzamide

PDB DOI: https://doi.org/10.2210/pdb5OIS/pdb

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

Deposited: 2017-07-19 Released: 2018-02-14
Deposition Author(s): Convery, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.189 (Depositor), 0.203 (DCC)
R-Value Work:
0.171 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.

Prati, F., Zuccotto, F., Fletcher, D., Convery, M.A., Fernandez-Menendez, R., Bates, R., Encinas, L., Zeng, J., Chung, C.W., De Dios Anton, P., Mendoza-Losana, A., Mackenzie, C., Green, S.R., Huggett, M., Barros, D., Wyatt, P.G., Ray, P.C.

(2018) ChemMedChem 13: 672-677

PubMed: 29399991 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201700774
Primary Citation Related Structures:
5OIC, 5OIF, 5OIL, 5OIM, 5OIN, 5OIO, 5OIP, 5OIQ, 5OIR, 5OIS, 5OIT

PubMed Abstract:
Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization.

Organizational Affiliation

Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, UK.

Macromolecule Content

Total Structure Weight: 118.24 kDa
Atom Count: 8,720
Modeled Residue Count: 1,072
Deposited Residue Count: 1,076
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A [auth B], B [auth D], C [auth F], D [auth H]	269	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: inhA, Rv1484, MTCY277.05 EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGR1 Go to UniProtKB: P9WGR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WGR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain J [auth F] SDF format, chain L [auth H] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain J [auth F] MOL2 format, chain L [auth H] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain J [auth F] mmCIF format, chain L [auth H]	F [auth B], H [auth D], J [auth F], L [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Focus chain J [auth F] Focus chain L [auth H] Interactions & Density Focus chain F [auth B] Focus chain H [auth D] Focus chain J [auth F] Focus chain L [auth H]
9WK (Subject of Investigation/LOI) Query on 9WK Download:Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain I [auth F] SDF format, chain G [auth D] SDF format, chain E [auth B] MOL2 format, chain K [auth H] MOL2 format, chain I [auth F] MOL2 format, chain G [auth D] MOL2 format, chain E [auth B] mmCIF format, chain K [auth H] mmCIF format, chain I [auth F] mmCIF format, chain G [auth D] mmCIF format, chain E [auth B]	E [auth B], G [auth D], I [auth F], K [auth H]	4-[(5-azanyl-3-methyl-pyrazol-1-yl)methyl]-~{N}-[(2-chloranyl-4-fluoranyl-phenyl)methyl]benzamide C₁₉ H₁₈ Cl F N₄ O HOVSFDUYYXXWGJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth D] Focus chain I [auth F] Focus chain K [auth H] Interactions & Density Focus chain E [auth B] Focus chain G [auth D] Focus chain I [auth F] Focus chain K [auth H]