9RJK | pdb_00009rjk

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV41a (compound 11)

• PDB DOI: https://doi.org/10.2210/pdb9RJK/pdb

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


• Deposited: 2025-06-12 Released: 2026-02-11 
• Deposition Author(s): Publicola, G., Mourey, L., Valderrama, K., Hartkoorn, R., Maveyraud, L.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Optimizing the Antibiotic Potency and Metabolic Stability of Pyridomycin Using a Semisynthetic Approach

Valderrama, K., Horlacher, O., Publicola, G., Eisenring, P., Kienle, M., Boarbi, S., Kiass, M., Kordulakova, J., Chatagnon, J., Piveteau, C., Leroux, F., Savkova, K., Zahorszka, M., Cantrelle, F.X., Lherbet, C., Mourey, L., Mikusova, K., Mathys, V., Aichholz, R., Maveyraud, L., Altmann, K.H., Hartkoorn, R.C.

(2026) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.5c02409

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.79 kDa 
• Atom Count: 8,671 
• Modeled Residue Count: 1,020 
• Deposited Residue Count: 1,088 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	272	Mycobacterium tuberculosis	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JG3 (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], J [auth D]	~{N}-[(2~{Z},5~{R},6~{S},9~{S},10~{S},11~{R})-2-butan-2-ylidene-5,11-dimethyl-10-oxidanyl-3,7,12-tris(oxidanylidene)-9-(pyridin-3-ylmethyl)-1,4-dioxa-8-azacyclododec-6-yl]-3-fluoranyl-2-oxidanyl-benzamide C28 H32 F N3 O8 SFZXQGFRHSUSNF-OYKKKHCWSA-N
PEG	F [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.07	α = 90
b = 81.35	β = 99.41
c = 95.48	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XSCALE	data scaling
TRUNCATE	data processing
BUSTER	refinement
PHASER	phasing
Coot	model building
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Publicola, G., Mourey, L., Valderrama, K., Hartkoorn, R., Maveyraud, L.

---

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-23-CE44-0002

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release