9RJK: Mycobacterium tuberculosis InhA

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative KV41a (compound 11). Determined by X-ray diffraction at 1.66 Å resolution. Released 11 Feb 2026.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: Mycobacterium tuberculosis
Chains: 4
Atoms: 8,671
Mol. weight: 117.79 kDa
Ligands: A1JG3
Released: 11 Feb 2026

Explore 9RJK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RJK contains 55 α-helices and 36 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	1
α-helix	21-31	11
α-helix	34	1
β-strand	35-40	6	1
α-helix	44-51	8
β-strand	60-62	3	1
α-helix	68-82	15
β-strand	88-93	6	1
α-helix	100-102	3
α-helix	108-110	3
α-helix	113-120	8
α-helix	121-125	5
α-helix	126-134	9
α-helix	135-137	3
β-strand	138-148	11	1
β-strand	154	1	2
α-helix	159-180	22
β-strand	185-191	7	1
α-helix	211-225	15
α-helix	236-246	11
β-strand	256-260	5	1
α-helix	264-266	3
β-strand	267	1	3

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	4
α-helix	21-31	11
α-helix	34	1
β-strand	35-40	6	4
α-helix	44-51	8
β-strand	60-62	3	4
α-helix	68-82	15
β-strand	88-93	6	4
α-helix	100-102	3
α-helix	108-110	3
α-helix	113-120	8
α-helix	121-125	5
α-helix	126-134	9
α-helix	135-137	3
β-strand	138-148	11	4
β-strand	154	1	5
α-helix	159-180	22
β-strand	185-191	7	4
α-helix	212-225	14
α-helix	236-246	11
β-strand	256-260	5	4
α-helix	264-266	3
β-strand	267	1	6

Chain C: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	7
α-helix	21-31	11
β-strand	35-40	6	7
α-helix	44-51	8
β-strand	60-62	3	7
α-helix	68-82	15
β-strand	88-93	6	7
α-helix	100-102	3
α-helix	108-110	3
α-helix	113-120	8
α-helix	121-125	5
α-helix	126-134	9
α-helix	135-137	3
β-strand	138-148	11	7
β-strand	154	1	6
α-helix	159-180	22
β-strand	185-191	7	7
α-helix	197-203	7
α-helix	210-225	16
α-helix	236-246	11
β-strand	256-260	5	7
α-helix	264-266	3
β-strand	267	1	5

Chain D: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	8
α-helix	22-31	10
β-strand	35-40	6	8
β-strand	60-62	3	8
α-helix	68-82	15
β-strand	88-93	6	8
α-helix	100-102	3
α-helix	108-110	3
α-helix	113-120	8
α-helix	121-125	5
α-helix	126-134	9
α-helix	135-137	3
β-strand	138-148	11	8
β-strand	154	1	3
α-helix	159-180	22
β-strand	185-191	7	8
α-helix	197-204	8
α-helix	209-225	17
α-helix	236-246	11
β-strand	256-260	5	8
α-helix	264-266	3
β-strand	267	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	protein	272	Mycobacterium tuberculosis	P9WGR1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9RJK_1 Enoyl-[acyl-carrier-protein] reductase [NADH] (chains A, B, C, D)
GSHMTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAK
APLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVS
KGIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVAR
EAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATP
VAKTVCALLSDWLPATTGDIIYADGGAHTQLL

Ligands and cofactors

ID	Name	Formula	Copies
A1JG3	~{N}-[(2~{Z},5~{R},6~{S},9~{S},10~{S},11~{R})-2-butan-2-ylidene-5,11-dimethyl-1…	C28 H32 F N3 O8	4

Water and common crystallization additives (PEG) are not listed.

Primary citation

Optimizing the Antibiotic Potency and Metabolic Stability of Pyridomycin Using a Semisynthetic Approach. Valderrama, K., Horlacher, O., Publicola, G. et al. J Med Chem (2026) 69:2496-2508. DOI 10.1021/acs.jmedchem.5c02409 · PubMed

Other PDB entries of the same protein (UniProt P9WGR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TRO 1.4 Å, Structure of the enoyl-ACP reductase of Mycobacterium tuberculosis InhA, inhibited with…
28IQ 1.51 Å, structure of InhA from Mycobacterium tuberculosis in complex with…
28IT 1.51 Å, structure of InhA from Mycobacterium tuberculosis in complex with…
5G0T 1.54 Å, InhA in complex with a DNA encoded library hit
28IP 1.59 Å, structure of InhA from Mycobacterium tuberculosis in complex with…
4OHU 1.6 Å, Crystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT92
8OTM 1.6 Å, structure of InhA from mycobacterium tuberculosis in complex with…
4TZK 1.62 Å, Crystal structure of Mycobacterium tuberculosis enoyl reductase (INHA) complexed WITH…
4U0J 1.62 Å, Crystal structure of Mycobacterium tuberculosis enoyl reductase (INHA) complexed with…
4D0S 1.64 Å, Mtb InhA complex with Pyradizinone compound 14
28IR 1.69 Å, structure of InhA from Mycobacterium tuberculosis in complex with…
9RJL 1.7 Å, Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative…

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