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- PDB-5oip: InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyr... -

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Basic information

Entry
Database: PDB / ID: 5oip
TitleInhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyrimidin-2-yl)piperidin-4-yl)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
Chem-9WE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
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)29,5964
Polymers28,5251
Non-polymers1,0713
Water5,477304
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)118,38216
Polymers114,0994
Non-polymers4,28312
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 area20130 Å2
ΔGint-173 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.140, 99.140, 141.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-497-

HOH

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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 (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-9WE / 1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea


Mass: 312.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% glycerol, 25% 1,2propanediol, 0.1M PO4. Cryo is well solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.71→41.34 Å / Num. obs: 45004 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 31.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Net I/σ(I): 19.6
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 17.1 % / Rmerge(I) obs: 2.876 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3248 / CC1/2: 0.514 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementResolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.966 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2157 4.8 %RANDOM
Rwork0.16 ---
obs0.161 44906 99.9 %-
Displacement parametersBiso mean: 36.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.398 Å20 Å20 Å2
2---3.398 Å20 Å2
3---6.7959 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.71→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 72 304 2370
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012196HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993013HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d749SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes343HARMONIC5
X-RAY DIFFRACTIONt_it2196HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion14.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion288SEMIHARMONIC5
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_contact2553SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 171 5.3 %
Rwork0.274 3058 -
all0.274 3229 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 45.8577 Å / Origin y: 48.705 Å / Origin z: -88.9066 Å
111213212223313233
T-0.0925 Å20.0146 Å2-0.013 Å2-0.056 Å20.0368 Å2---0.0401 Å2
L0.5791 °20.0456 °20.0819 °2-0.3907 °2-0.0195 °2--0.8978 °2
S-0.0447 Å °-0.057 Å °0.0315 Å °-0.0017 Å °-0.0467 Å °-0.0998 Å °-0.0716 Å °0.279 Å °0.0914 Å °
Refinement TLS groupSelection details: { A|* }

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