9Z09 | pdb_00009z09

Crystal structure of M. tuberculosis ProRS bound to 3-(4-bromobenzamido)pyrazine-2-carboxamide (compound 4e)

PDB DOI: https://doi.org/10.2210/pdb9Z09/pdb

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

Deposited: 2025-10-31 Released: 2026-11-04
Deposition Author(s): Gade, P., Michalska, K., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Atomic-Level Structures Reveal How a Repurposed 3‐Aminopyrazine-2-carboxamide Scaffold Inhibits Mycobacterium tuberculosis Prolyl-tRNA Synthetase.

Gade, P., Michalska, K., Zitko, J., Wower, J., Maltseva, N., Pallabothula, V.S.K., Jedrzejczak, R., Joachimiak, A.

(2026) ACS Omega 11: 57583-57594

PubMed: 42825133 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsomega.6c04844
Primary Citation Related Structures:
9YXS, 9YY6, 9YYE, 9YYF, 9YYO, 9YYT, 9YZX, 9Z09

PubMed Abstract:
Tuberculosis (TB) is again the world's leading cause of death from a single infectious agent. Aminoacyl-tRNA synthetases are essential for protein synthesis and are promising drug targets because bacterial and human enzymes differ. We repurposed a human prolyl-tRNA synthetase (ProRS) inhibitor scaffold, 3-aminopyrazine-2-carboxamide, to inhibit the Mycobacterium tuberculosis enzyme ( Mtb ProRS). These derivatives show strong activity against multidrug-resistant Mtb strains and are not cytotoxic to HepG2 cells. We determined high-resolution crystal structures of Mtb ProRS bound to six derivatives to define their binding modes. The compounds bind in the ATP site and trigger local conformational changes that disrupt the proline pocket, supporting a dual-site mechanism of inhibition. Comparison with human cytosolic and mitochondrial ProRS reveals differences in active-site residues, electrostatics, and dynamics that explain species selectivity. Together, these structures provide a framework for designing next-generation, Mtb -selective ProRS inhibitors as new antitubercular candidates.

Organizational Affiliation

Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States.

Macromolecule Content

Total Structure Weight: 129.36 kDa
Atom Count: 8,749
Modeled Residue Count: 1,122
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline--tRNA ligase	A, B	588	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: proS, Rv2845c, MTCY24A1.12 EC: 6.1.1.15
UniProt
Find proteins for P9WFT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFT9 Go to UniProtKB: P9WFT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WFT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CZT (Subject of Investigation/LOI) Query on A1CZT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	3-(4-bromobenzamido)pyrazine-2-carboxamide C₁₂ H₉ Br N₄ O₂ SAZAWTYKBYDDJF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]