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- PDB-4uve: Discovery of pyrimidine isoxazoles InhA in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 4uve
TitleDiscovery of pyrimidine isoxazoles InhA in complex with compound 9
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
2-(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYLETHANOL / 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: 1.99 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
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4274
Polymers28,5551
Non-polymers8723
Water5,495305
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)117,70716
Polymers114,2194
Non-polymers3,48812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
crystal symmetry operation4_765-x+2,-y+1,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area21510 Å2
ΔGint-145.1 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.469, 97.469, 140.698
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-2149-

HOH

21A-2186-

HOH

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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.: 1
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


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KI5 / 2-(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYLETHANOL


Mass: 184.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 3.38 Å3/Da / Density % sol: 63.59 % / 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: Sep 19, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.99→97.5 Å / Num. obs: 177948 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.5
Reflection shellResolution: 1.99→2.09 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.1 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D0R

4d0r


Resolution: 1.99→72.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.41 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17487 1288 5 %RANDOM
Rwork0.14877 ---
obs0.15007 24363 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.67 Å20 Å2
2--0.67 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.99→72.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 57 305 2354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192106
X-RAY DIFFRACTIONr_bond_other_d0.0010.022032
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.992869
X-RAY DIFFRACTIONr_angle_other_deg0.8734660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60623.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0421514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02466
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 98 -
Rwork0.2 1790 -
obs--95.21 %
Refinement TLS params.Method: refined / Origin x: 51.8091 Å / Origin y: 47.6872 Å / Origin z: 18.3373 Å
111213212223313233
T0.0115 Å20.0088 Å2-0.0086 Å2-0.0635 Å2-0.0234 Å2--0.0225 Å2
L0.1948 °20.004 °20.0567 °2-0.1 °20.0633 °2--0.2422 °2
S-0.0349 Å °0.0269 Å °-0.0005 Å °0.0052 Å °-0.0297 Å °0.0018 Å °-0.0344 Å °-0.0886 Å °0.0646 Å °

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