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- PDB-4uvi: Discovery of pyrimidine isoxazoles InhA in complex with compound 23 -

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Basic information

Entry
Database: PDB / ID: 4uvi
TitleDiscovery of pyrimidine isoxazoles InhA in complex with compound 23
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / INHA / ACP ENOYL REDUCTASE / FBLG / PYRIMIDINE ISOXAZOLE
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 / fatty acid biosynthetic process / 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-KXU / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRead, J.A. / Gingell, H. / Madhavapeddi, P. / Ghorpade, S. / Cowan, S.
CitationJournal: To be Published
Title: Hitting the Target in More Than One Way: Novel, Direct Inhibitors of Mycobacterium Tuberculosis Enoyl Acp Reductase
Authors: Madhavapeddi, P. / Kale, R.R. / Cowen, S.D. / Ghorpade, S.R. / Davies, G. / Bellale, E.V. / Kale, M.G. / Srivastava, A. / Spadola, L. / Kawatkar, A. / Raichurkar, A.V. / Tonge, M. / ...Authors: Madhavapeddi, P. / Kale, R.R. / Cowen, S.D. / Ghorpade, S.R. / Davies, G. / Bellale, E.V. / Kale, M.G. / Srivastava, A. / Spadola, L. / Kawatkar, A. / Raichurkar, A.V. / Tonge, M. / Nandishaiah, R. / Guptha, S. / Narayan, A. / Gingell, H. / Plant, D. / Landge, S. / Menasinakai, S. / Prabhakar, K.R. / Achar, V. / Ambady, A. / Sambandamurthy, V.K. / Ramachandran, V. / Panduga, V. / Reddy, J. / Kumar, C.N.N. / Kaur, P. / Shandil, R. / Iyer, P.S. / Narayanan, S. / Read, J.A.
History
DepositionAug 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)118,35112
Polymers114,2194
Non-polymers4,1318
Water15,817878
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-132.8 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.144, 111.656, 67.723
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / ENOYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR
References: UniProt: M9TGV3, UniProt: P9WGR1*PLUS, 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-KXU / 5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-N-[(2-methylpyridin-4-yl)methyl]-1,2-oxazole-3-carboxamide


Mass: 369.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19N5O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.13 Å3/Da / Density % sol: 42.31 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 21, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.73→77 Å / Num. obs: 331121 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 19.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 91.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→66.96 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 4764 5 %RANDOM
Rwork0.1688 ---
obs0.17 95241 95.58 %-
Displacement parametersBiso mean: 20.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.9844 Å20 Å2-0.2631 Å2
2---0.1924 Å20 Å2
3----0.792 Å2
Refinement stepCycle: LAST / Resolution: 1.73→66.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7618 0 280 878 8776
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018091HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0111045HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2675SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes159HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1284HARMONIC5
X-RAY DIFFRACTIONt_it8091HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion15.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1098SEMIHARMONIC5
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_contact10041SEMIHARMONIC4
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3624 270 4.51 %
Rwork0.3088 5714 -
all0.3111 5984 -
obs--95.58 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
10.201113.453628.6247
223.0261-19.408412.6874
34.93912.0853-1.4256
428.93512.944734.9305
514.5043-0.036118.7045

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