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- PDB-5oil: InhA (T2A mutant) complexed with 1-cyclohexyl-3-(pyridin-3-ylmeth... -

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Basic information

Entry
Database: PDB / ID: 5oil
TitleInhA (T2A mutant) complexed with 1-cyclohexyl-3-(pyridin-3-ylmethyl)urea
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Inhibitor / complex / fragment based drug discovery / tuberculosis
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 / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-cyclohexyl-3-(pyridin-3-ylmethyl)urea / 2-ETHOXYETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.76 Å
AuthorsConvery, M.A.
CitationJournal: ChemMedChem / Year: 2018
Title: Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA.
Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / ...Authors: Prati, F. / Zuccotto, F. / Fletcher, D. / Convery, M.A. / Fernandez-Menendez, R. / Bates, R. / Encinas, L. / Zeng, J. / Chung, C.W. / De Dios Anton, P. / Mendoza-Losana, A. / Mackenzie, C. / Green, S.R. / Huggett, M. / Barros, D. / Wyatt, P.G. / Ray, P.C.
History
DepositionJul 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5124
Polymers28,5251
Non-polymers9873
Water3,729207
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,04616
Polymers114,0994
Non-polymers3,94712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_553y,x,-z-4/31
crystal symmetry operation10_663-y+1,-x+1,-z-4/31
Buried area19000 Å2
ΔGint-135 kcal/mol
Surface area34180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.500, 97.500, 140.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 28524.754 Da / Num. of mol.: 1 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-9VW / 1-cyclohexyl-3-(pyridin-3-ylmethyl)urea


Mass: 233.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N3O
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 35-42% Ethoxyethanol and 0.1M Mes pH 6.5-6.8. 5% glycerol used as cryoprotectant. Crystals were soaked to obtain ligand complex.
PH range: 6.5-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.76→46.77 Å / Num. obs: 10717 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 51.38 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.251 / Net I/σ(I): 9.6
Reflection shellResolution: 2.76→2.95 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1885 / CC1/2: 0.818 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementResolution: 2.76→46.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.514 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.839 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.23 523 4.9 %RANDOM
Rwork0.154 ---
obs0.157 10670 99.8 %-
Displacement parametersBiso mean: 30.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.7427 Å20 Å20 Å2
2---2.7427 Å20 Å2
3---5.4855 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.76→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 67 207 2263
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012116HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.162878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d731SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes333HARMONIC5
X-RAY DIFFRACTIONt_it2116HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.87
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion281SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2648SEMIHARMONIC4
LS refinement shellResolution: 2.76→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.313 129 4.39 %
Rwork0.17 2811 -
all0.176 2940 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 45.2767 Å / Origin y: 47.8707 Å / Origin z: -88.2972 Å
111213212223313233
T-0.089 Å2-0.006 Å2-0.0205 Å2-0.1042 Å20.0396 Å2---0.0975 Å2
L0.7167 °2-0.1732 °20.1334 °2-0.4805 °2-0.1629 °2--0.7409 °2
S-0.0673 Å °-0.0274 Å °0.1002 Å °0.006 Å °-0.0263 Å °-0.1102 Å °-0.0752 Å °0.3046 Å °0.0936 Å °
Refinement TLS groupSelection details: { A|* }

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