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

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Basic information

Entry
Database: PDB / ID: 28lm
Titlestructure of InhA from Mycobacterium tuberculosis in complex with 4-(4-((4-butyl-1H-1,2,3-triazol-1-yl)methyl)-2-hydroxyphenoxy)-3-fluorobenzaldehyde (compound 5f)
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
: / ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTamhaev, R. / Valentin, L. / 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 5, 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]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,07726
Polymers230,6968
Non-polymers8,38118
Water20,3031127
1
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)119,53913
Polymers115,3484
Non-polymers4,1909
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-128 kcal/mol
Surface area31950 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,53913
Polymers115,3484
Non-polymers4,1909
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19290 Å2
ΔGint-130 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.69, 76.23, 109.21
Angle α, β, γ (deg.)86.71, 72.16, 90.09
Int Tables number1
Space group name H-MP1

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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.: 8
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.: 8 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-A1JZS / 4-[4-[(4-butyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]-3-fluoranyl-benzaldehyde


Mass: 369.390 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H20FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1127 / 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: 2.32 Å3/Da / Density % sol: 47 %
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: 0.885602 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: 0.885602 Å / Relative weight: 1
ReflectionResolution: 1.96→76.09 Å / Num. obs: 145519 / % possible obs: 97.8 % / Redundancy: 3.39 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1444 / Rpim(I) all: 0.0919 / Rrim(I) all: 0.1717 / Net I/σ(I): 6.55
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.32-76.0893.480.051617.462570525705737973790.997-0.1270.03240.06110.76296.91.7798.9
4.223-5.323.290.059715.812382823828724772470.994-0.1140.03860.07140.778921.797.7
3.689-4.2233.130.065314.372265022650724572450.993-0.0570.04370.0790.80289.71.6397.2
3.352-3.6893.360.082312.732459424594732573250.99-0.0840.05250.09790.82193.11.7398.2
3.112-3.3523.450.103710.532521825218731473140.986-0.010.0650.12270.82993.81.7798.3
2.928-3.1123.480.13918.362542525425730073000.976-0.0220.08710.16450.82794.41.7898.3
2.782-2.9283.520.16177.282581725817734473440.97-0.0170.10040.19070.83394.71.7998.2
2.66-2.7823.540.19626.172589125891731673160.955-0.0130.12170.23130.814951.898.2
2.558-2.663.410.22335.362482924829727972790.9440.0070.14140.2650.816941.7598.1
2.47-2.5583.220.2624.412361623616732773270.915-0.0210.17280.31530.80492.81.6698.1
2.393-2.473.40.28144.342452924529722272220.916-0.0180.17950.33490.80993.71.7497.7
2.324-2.3933.460.31143.942520025200727672760.905-00.1950.36830.79794.41.7798
2.263-2.3243.250.35163.382355923559725572550.86-0.0010.2290.42130.791921.6896.9
2.208-2.2633.20.37583.152318423184725572550.8520.0420.24830.45250.80292.11.6597.3
2.158-2.2083.340.41072.982433124331729272920.830.0030.26490.49050.79493.41.7197.7
2.112-2.1583.410.49582.562453524535719171910.788-0.0140.31290.58780.79293.71.7597.4
2.069-2.1123.450.5722.242491624916722172210.722-0.0160.35840.67670.7793.81.7797.2
2.03-2.0693.460.61552.092530125301731573150.7040.0050.38710.7290.784941.7697.4
1.994-2.033.480.66531.922492224922715971590.676-0.0310.4160.78650.76594.41.7797.2
1.96-1.9943.490.76751.652531725317725772570.636-0.0340.48050.90770.76994.21.7797.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 20230726data processing
XSCALEdata scaling
TRUNCATE9.0.003data processing
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→76.09 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 7339 -RANDOM
Rwork0.1957 138179 --
obs0.1969 145518 97.7 %-
Displacement parametersBiso mean: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.7275 Å23.2513 Å21.8611 Å2
2---0.3492 Å2-3.3877 Å2
3---2.0768 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 1.96→76.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15574 0 576 1127 17277
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00816589HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9222630HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5554SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2907HARMONIC5
X-RAY DIFFRACTIONt_it16589HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2230SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact15523SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion14.85
LS refinement shellResolution: 1.96→1.97 Å
RfactorNum. reflection% reflection
Rfree0.3307 171 -
Rwork0.2639 2740 -
obs0.2679 2911 94.65 %
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)
10.59270.2252-0.06710.791-0.25010.7776-0.03980.01270.0612-0.06460.01390.0327-0.16580.02520.02590.0352-0.01350.0137-0.0933-0.0016-0.0484-30.3389-17.0356-49.8632
20.69930.48360.06081.1284-0.10570.75460.0235-0.0172-0.1242-0.0133-0.0754-0.2108-0.01190.13230.052-0.0880.01830.0293-0.06340.00550.025-18.4985-43.9759-36.9296
30.69460.1523-0.09191.245-0.16960.4772-0.01130.0042-0.1007-0.0381-0.00020.13950.0555-0.03920.0115-0.0770.01080.0251-0.0858-0.02390.0233-48.9505-53.9526-37.3313
40.77430.2790.01010.9435-0.29360.8211-0.10160.16460.0167-0.32130.12770.16790.0303-0.0916-0.02610.0556-0.0445-0.0652-0.04360.0009-0.0771-51.1114-37.067-64.3555
50.61360.06870.00610.76450.1240.44190.0373-0.0094-0.12370.0329-0.044-0.10510.02160.03150.0067-0.06860.00140.0155-0.0811-0.00850.032211.9367-15.8278-9.787
60.6150.00430.08350.8008-0.13830.7330.05610.0173-0.04870.0306-0.02730.1306-0.0071-0.0984-0.0288-0.07410.00470.0258-0.0719-0.02870.0133-18.6859-5.8636-10.0288
70.72860.0892-0.02080.59630.02490.790.0204-0.00240.08330.1181-0.02970.025-0.29960.00570.00920.0834-0.01530.0312-0.114-0.0151-0.0505-6.838921.01373.1394
80.46930.0230.05540.60240.09030.74070.0648-0.118-0.0760.1839-0.0633-0.053-0.12030.1057-0.00150.0591-0.0903-0.0284-0.03450.017-0.076114.44621.17317.3153
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|* }B3 - 269
4X-RAY DIFFRACTION2{ B|* }B301 - 303
5X-RAY DIFFRACTION3{ C|* }C3 - 269
6X-RAY DIFFRACTION3{ C|* }C301 - 302
7X-RAY DIFFRACTION4{ D|* }D2 - 269
8X-RAY DIFFRACTION4{ D|* }D301 - 302
9X-RAY DIFFRACTION5{ E|* }E3 - 269
10X-RAY DIFFRACTION5{ E|* }E301 - 302
11X-RAY DIFFRACTION6{ F|* }F3 - 269
12X-RAY DIFFRACTION6{ F|* }F301 - 303
13X-RAY DIFFRACTION7{ G|* }G3 - 269
14X-RAY DIFFRACTION7{ G|* }G301 - 302
15X-RAY DIFFRACTION8{ H|* }H3 - 269
16X-RAY DIFFRACTION8{ H|* }H301 - 302

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