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- PDB-5oin: InhA (T2A mutant) complexed with N-(1-(pyrimidin-2-yl)piperidin-4... -

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Basic information

Entry
Database: PDB / ID: 5oin
TitleInhA (T2A mutant) complexed with N-(1-(pyrimidin-2-yl)piperidin-4-yl)acetamide
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
~{N}-(1-pyrimidin-2-ylpiperidin-4-yl)ethanamide / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.82 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

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)117,41411
Polymers114,0994
Non-polymers3,3157
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18830 Å2
ΔGint-133 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.070, 101.080, 186.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-9W2 / ~{N}-(1-pyrimidin-2-ylpiperidin-4-yl)ethanamide


Mass: 220.271 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H16N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.81 Å3/Da / Density % sol: 67.74 %
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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.82→82.6 Å / Num. obs: 42892 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 80.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3
Reflection shellResolution: 2.82→2.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.08 / Num. unique obs: 3145 / CC1/2: 0.474 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementResolution: 2.82→82.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2183 5.1 %RANDOM
Rwork0.16 ---
obs0.161 42829 100 %-
Displacement parametersBiso mean: 86.68 Å2
Baniso -1Baniso -2Baniso -3
1--4.5132 Å20 Å20 Å2
2---10.4033 Å20 Å2
3---14.9165 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.82→82.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 224 77 8144
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018238HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.111235HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2754SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1302HARMONIC5
X-RAY DIFFRACTIONt_it8238HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1116SEMIHARMONIC5
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_contact9488SEMIHARMONIC4
LS refinement shellResolution: 2.82→2.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 140 4.47 %
Rwork0.256 2993 -
all0.258 3133 -
obs--99.9 %
Refinement TLS params.

Method: refined / 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)
10.1877-0.1246-0.13440.39490.26934.00520.030.25810.02260.0039-0.196-0.00130.0399-0.06880.166-0.131-0.0315-0.0398-0.0850.0031-0.037-45.091524.7985-23.2666
21.3971-0.16160.32070.9826-0.12632.1569-0.0675-0.0388-0.0351-0.01730.0009-0.27870.1660.66320.0666-0.12680.00540.00230.13680.0312-0.1795-23.506120.5835-19.2078
31.07770.1748-0.16331.03730.46082.3508-0.0612-0.09780.13920.0028-0.06450.351-0.0844-0.62430.1258-0.1382-0.03920.01070.1151-0.0768-0.1481-66.244328.9196-17.2583
41.41370.1032-0.11851.33260.23142.51560.00610.0619-0.24640.0677-0.12180.02370.6881-0.00190.11580.2048-0.09190.0177-0.1905-0.0509-0.2254-48.87193.4739-28.0935
51.0783-0.02110.13321.59860.20122.64030.03950.02620.3232-0.0325-0.1546-0.1303-0.65020.0470.11510.1298-0.101-0.0358-0.14830.0595-0.1784-41.551246.2359-28.43
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ B|* }
4X-RAY DIFFRACTION4{ C|* }
5X-RAY DIFFRACTION5{ D|* }

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