8OTM: InhA from mycobacterium tuberculosis

structure of InhA from mycobacterium tuberculosis in complex with N-((1-(3-hydroxy-4-phenoxybenzyl)-1H-1,2,3-triazol-4-yl)methyl)-2-oxo-2H-chromene-3-carboxamide. Determined by X-ray diffraction at 1.6 Å resolution. Released 16 Aug 2023.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mycobacterium tuberculosis
Chains: 4
Atoms: 9,655
Mol. weight: 119.68 kDa
Ligands: NAD, VZI
Released: 16 Aug 2023

Explore 8OTM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OTM contains 70 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
α-helix	21-31	11
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	197	1
α-helix	198-204	7
α-helix	205-207	3
α-helix	208-210	3
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: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	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	197	1
α-helix	198-204	7
α-helix	205-207	3
α-helix	208-210	3
α-helix	211-225	15
α-helix	236-246	11
β-strand	257-260	4	4
α-helix	264-266	3
β-strand	267	1	6

Chain C: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	7
α-helix	21-31	11
α-helix	34	1
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	3
α-helix	159-180	22
β-strand	185-191	7	7
α-helix	197-198	2
α-helix	199-203	5
α-helix	204-210	7
α-helix	211-225	15
α-helix	236-246	11
β-strand	256-260	5	7
α-helix	264-266	3
β-strand	267	1	2

Chain D: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	8
α-helix	21-31	11
α-helix	34	1
β-strand	35-40	6	8
α-helix	44-51	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	6
α-helix	159-180	22
β-strand	185-191	7	8
α-helix	197	1
α-helix	198-203	6
α-helix	204-207	4
α-helix	208-210	3
α-helix	211-225	15
α-helix	236-246	11
β-strand	256-260	5	8
α-helix	264-266	3
β-strand	267	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	protein	271	Mycobacterium tuberculosis	P9WGR1 (AlphaFold model)

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

>8OTM_1 Enoyl-[acyl-carrier-protein] reductase [NADH] (chains A, B, C, D)
GSMTGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKA
PLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSK
GIHISAYSYASMAKALLPIMNPGGSIVGMDFDPSRAMPAYNWMTVAKSALESVNRFVARE
AGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPV
AKTVCALLSDWLPATTGDIIYADGGAHTQLL

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	4
VZI	2-oxidanylidene-~{N}-[[1-[(3-oxidanyl-4-phenoxy-phenyl)methyl]-1,2,3-triazol-4-…	C26 H20 N4 O5	4

Water and common crystallization additives (ACT, NA, EDO) are not listed.

Primary citation

Discovery of new diaryl ether inhibitors against Mycobacterium tuberculosis targeting the minor portal of InhA. Chebaiki, M., Delfourne, E., Tamhaev, R. et al. Eur J Med Chem (2023) 259:115646-115646. DOI 10.1016/j.ejmech.2023.115646 · 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
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
9RJK 1.66 Å, Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin derivative…
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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