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- PDB-28ir: structure of InhA from Mycobacterium tuberculosis in complex with... -

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Basic information

Entry
Database: PDB / ID: 28ir
Titlestructure of InhA from Mycobacterium tuberculosis in complex with 4-(4-((4-cyclopropyl-1H-1,2,3-triazol-1-yl)methyl)-2-hydroxyphenoxy)-3-fluorobenzaldehyde (compound 5c)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / ENOYL-ACP-REDUCTASE TYPE II FATTY ACID SYNTHASE MYCOLIC ACIDS TUBERCULOSIS THERAPEUTIC TARGET OXIDOREDUCTASE
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsTamhaev, R. / Lherbet, C. / Azema-Despeyroux, J. / Mourey, L. / Maveyraud, L.
Funding support France, Italy, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-23-CE44-0002 France
Universite de Toulouse France
La Region Occitanie Italy
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: J.Med.Chem. / Year: 2026
Title: Rational Design of Diaryl Ether-Based Dual Inhibitors Targeting Successive Essential Enzymes HadAB and InhA in Mycobacterium tuberculosis.
Authors: Tamhaev, R. / Recchia, D. / Zahorszka, M. / Stelitano, G. / Chiarelli, L.R. / Rizet, J. / Rima, J. / Chebaiki, M. / Valentin, L. / Azema-Despeyroux, J. / Hoffmann, P. / Preuilh, N. / Dumais, ...Authors: Tamhaev, R. / Recchia, D. / Zahorszka, M. / Stelitano, G. / Chiarelli, L.R. / Rizet, J. / Rima, J. / Chebaiki, M. / Valentin, L. / Azema-Despeyroux, J. / Hoffmann, P. / Preuilh, N. / Dumais, B. / Britton, S. / Degiacomi, G. / Maveyraud, L. / Kordulakova, J. / Pasca, M.R. / Mourey, L. / Lherbet, C.
History
DepositionFeb 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,41512
Polymers115,3484
Non-polymers4,0678
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18890 Å2
ΔGint-133 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.122, 91.828, 103.203
Angle α, β, γ (deg.)90, 105.2, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-614-

HOH

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / ENR / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 28837.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Plasmid: pET15b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-A1JZB / 4-(4-((4-cyclopropyl-1H-1,2,3-triazol-1-yl)methyl)-2-hydroxyphenoxy)-3-fluorobenzaldehyde / 4-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]-3-fluoranyl-benzaldehyde


Mass: 353.347 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H16FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: PEG 4000 14 % (w/v) ADA buffer 0.1 M Ammonium Acetate 0.1 M DMSO 5 % (v/v) NAD+ 1.4 mM Compound 2.5 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.69→73.305 Å / Num. obs: 97054 / % possible obs: 76.5 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Net I/σ(I): 10.8
Reflection shell

Num. unique obs: 4853 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
5.06-73.3057.20.0433.20.9990.0340.09100
1.69-1.8387.50.9561.40.8180.3731.02617.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
autoPROCdata processing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENY

1eny


Resolution: 1.69→73.305 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 5000 -RANDOM
Rwork0.1757 92054 --
obs0.1765 97054 76.5 %-
Displacement parametersBiso mean: 29.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.1222 Å20 Å2-0.2445 Å2
2---0.4319 Å20 Å2
3---0.5541 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.69→73.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7756 0 280 960 8996
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098439HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9211524HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2901SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1487HARMONIC5
X-RAY DIFFRACTIONt_it8439HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1127SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies21HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8586SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion14.56
LS refinement shellResolution: 1.69→1.79 Å
RfactorNum. reflection% reflection
Rfree0.2455 110 -
Rwork0.246 1832 -
obs0.2459 1942 9.72 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0185-0.3680.11751.0821-0.05340.49170.06330.0489-0.2635-0.1118-0.07580.06280.08770.08210.0125-0.07210.0753-0.0057-0.0908-0.021-0.0530.99240.36719.5659
21.3793-0.5455-0.0281.3623-0.03690.43090.0498-0.0081-0.1835-0.0487-0.04620.3234-0.0562-0.0861-0.0036-0.09960.0547-0.0072-0.083-0.0239-0.05125.481920.475623.1254
31.1768-0.01030.13750.9631-0.2140.60650.01110.08320.2867-0.0301-0.0547-0.0128-0.20610.05780.0436-0.01410.02090.0015-0.13040.0172-0.079326.01143.52615.7866
41.0538-0.01480.25890.9592-0.03930.7799-0.0112-0.0450.05910.0782-0.0536-0.2245-0.10590.23580.0647-0.1067-0.0105-0.0256-0.00660.0241-0.090148.44524.736830.7542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 269
2X-RAY DIFFRACTION1{ A|* }A301 - 302
3X-RAY DIFFRACTION2{ B|* }B2 - 269
4X-RAY DIFFRACTION2{ B|* }B301 - 302
5X-RAY DIFFRACTION3{ C|* }C2 - 269
6X-RAY DIFFRACTION3{ C|* }C301 - 302
7X-RAY DIFFRACTION4{ D|* }D3 - 269
8X-RAY DIFFRACTION4{ D|* }D301 - 302

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