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- PDB-4qxm: Crystal structure of the InhA:GSK_SB713 complex -

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Basic information

Entry
Database: PDB / ID: 4qxm
TitleCrystal structure of the InhA:GSK_SB713 complex
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossman fold / enoyl-ACP reductase / NADH binding / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-713 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsGulten, G. / Sacchettini, J.C.
CitationJournal: Chemmedchem / Year: 2016
Title: N-Benzyl-4-((heteroaryl)methyl)benzamides: A New Class of Direct NADH-Dependent 2-trans Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors with Antitubercular Activity.
Authors: Guardia, A. / Gulten, G. / Fernandez, R. / Gomez, J. / Wang, F. / Convery, M. / Blanco, D. / Martinez, M. / Perez-Herran, E. / Alonso, M. / Ortega, F. / Rullas, J. / Calvo, D. / Mata, L. / ...Authors: Guardia, A. / Gulten, G. / Fernandez, R. / Gomez, J. / Wang, F. / Convery, M. / Blanco, D. / Martinez, M. / Perez-Herran, E. / Alonso, M. / Ortega, F. / Rullas, J. / Calvo, D. / Mata, L. / Young, R. / Sacchettini, J.C. / Mendoza-Losana, A. / Remuinan, M. / Ballell Pages, L. / Castro-Pichel, J.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,61610
Polymers114,2194
Non-polymers3,3976
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18480 Å2
ΔGint-128 kcal/mol
Surface area33510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.359, 83.627, 86.037
Angle α, β, γ (deg.)90.00, 115.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / NADH-dependent enoyl-ACP reductase / Enoyl-ACP reductase InhA


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: inhA, MTCY277.05, Rv1484 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-713 / N-(2-chloro-4-fluorobenzyl)-4-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]benzamide


Mass: 371.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19ClFN3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M N-(2-acetamido)iminodiacetic acid, pH 6.8, 6% v/v DMSO, 16% w/v PEG3350, 0.18 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.196→77.776 Å / Num. all: 55342 / Num. obs: 48167 / % possible obs: 86.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 32.15 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.2
Reflection shellResolution: 2.196→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.53 / % possible all: 60.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ENY

1eny


Resolution: 2.196→45.575 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 2444 5.1 %RANDOM
Rwork0.1914 ---
obs0.193 47941 86.63 %-
all-48167 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→45.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7693 0 228 339 8260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068090
X-RAY DIFFRACTIONf_angle_d1.08411019
X-RAY DIFFRACTIONf_dihedral_angle_d14.2082957
X-RAY DIFFRACTIONf_chiral_restr0.0721248
X-RAY DIFFRACTIONf_plane_restr0.0051406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.196-2.24070.2988920.26261738X-RAY DIFFRACTION56
2.2407-2.28940.248970.26041948X-RAY DIFFRACTION63
2.2894-2.34260.2898910.24342097X-RAY DIFFRACTION68
2.3426-2.40120.29931280.24772192X-RAY DIFFRACTION71
2.4012-2.46610.2851330.23532282X-RAY DIFFRACTION75
2.4661-2.53870.2911200.23992498X-RAY DIFFRACTION81
2.5387-2.62060.28631300.23162636X-RAY DIFFRACTION86
2.6206-2.71430.23521380.22612773X-RAY DIFFRACTION90
2.7143-2.82290.26531870.21782873X-RAY DIFFRACTION94
2.8229-2.95140.27631680.21642971X-RAY DIFFRACTION97
2.9514-3.1070.27371770.2222996X-RAY DIFFRACTION98
3.107-3.30160.23171640.20793025X-RAY DIFFRACTION98
3.3016-3.55640.20331600.19593054X-RAY DIFFRACTION99
3.5564-3.91410.23991470.1713079X-RAY DIFFRACTION99
3.9141-4.48010.18321870.15223070X-RAY DIFFRACTION100
4.4801-5.64280.16351700.15483103X-RAY DIFFRACTION99
5.6428-45.58490.17721550.16793162X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -17.0224 Å / Origin y: -3.693 Å / Origin z: 15.5926 Å
111213212223313233
T0.3451 Å20.0206 Å2-0.0099 Å2-0.1424 Å2-0.0252 Å2--0.1938 Å2
L0.6782 °2-0.0093 °2-0.1775 °2-1.143 °2-0.033 °2--0.5889 °2
S-0.0026 Å °0.1692 Å °-0.0683 Å °-0.4298 Å °-0.0379 Å °0.0396 Å °0.0027 Å °-0.0662 Å °0.0246 Å °
Refinement TLS groupSelection details: all

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