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

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Basic information

Entry
Database: PDB / ID: 28iq
Titlestructure of InhA from Mycobacterium tuberculosis in complex with 4-(4-hexyl-2-hydroxyphenoxy)benzaldehyde (compound 5a) - spacegroup P41212
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: 1.513 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)119,35214
Polymers115,3484
Non-polymers4,00310
Water17,024945
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19340 Å2
ΔGint-132 kcal/mol
Surface area32790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.2, 90.2, 289.04
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-440-

HOH

21B-621-

HOH

31D-457-

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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-A1JY8 / 4-(4-hexyl-2-hydroxyphenoxy)benzaldehyde / 4-(4-hexyl-2-oxidanyl-phenoxy)benzaldehyde


Mass: 298.376 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H22O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
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+ 28 mM Compound 28 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.513→86.105 Å / Num. obs: 180007 / % possible obs: 96.8 % / Redundancy: 23.8 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.015 / Rrim(I) all: 0.077 / Net I/σ(I): 27.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.107-86.10522.50.04168.599860.9990.0090.042100
1.513-1.53914.30.9712.767880.6660.2521.00774

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
Aimless0.7.15data scaling
autoPROCdata processing
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.513→86.105 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 8957 -RANDOM
Rwork0.1642 171025 --
obs0.1651 179982 96.8 %-
Displacement parametersBiso mean: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.5345 Å20 Å20 Å2
2--1.5345 Å20 Å2
3----3.0689 Å2
Refine analyzeLuzzati coordinate error obs: 0.165 Å
Refinement stepCycle: LAST / Resolution: 1.513→86.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 272 945 8895
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018299HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0311335HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2847SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1461HARMONIC5
X-RAY DIFFRACTIONt_it8299HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1132SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies27HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8696SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.27
X-RAY DIFFRACTIONt_other_torsion14.07
LS refinement shellResolution: 1.513→1.53 Å
RfactorNum. reflection% reflection
Rfree0.2461 176 -
Rwork0.2342 3424 -
obs--72.19 %
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)
10.115-0.0531-0.15060.28630.04820.1176-0.00310.0080.0038-0.07020.0115-0.0686-0.0129-0.0119-0.00840.02580.00820.01980.0086-0.015-0.029533.600762.21893.1454
20.08050.11090.02330.42990.08320.1373-0.0173-0.00070.0217-0.0158-0.00260.0352-0.03070.0240.01990.03910.0172-0.0146-0.01570.0008-0.031416.80184.845118.311
30.2360.0209-0.14680.3986-0.01440.0635-0.04810.0133-0.0280.0134-0.0053-0.01060.03-0.01320.05340.03670.011-0.0064-0.0127-0.0216-0.031714.819941.308820.204
40.28260.0812-0.03560.23920.02460.0630.00260.02240.0348-0.003-0.03950.08750.0166-0.03640.0368-0.0170.015-0.02090.0168-0.02390.0082-7.941863.681417.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 269
2X-RAY DIFFRACTION1{ A|* }A301 - 303
3X-RAY DIFFRACTION1{ A|* }A401 - 643
4X-RAY DIFFRACTION2{ B|* }B1 - 269
5X-RAY DIFFRACTION2{ B|* }B301 - 303
6X-RAY DIFFRACTION2{ B|* }B401 - 641
7X-RAY DIFFRACTION3{ C|* }C2 - 269
8X-RAY DIFFRACTION3{ C|* }C301 - 302
9X-RAY DIFFRACTION3{ C|* }C401 - 649
10X-RAY DIFFRACTION4{ D|* }D3 - 269
11X-RAY DIFFRACTION4{ D|* }D301 - 302
12X-RAY DIFFRACTION4{ D|* }D401 - 612

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