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- PDB-6i47: Structure of P. aeruginosa LpxC with compound 10: (2RS)-4-(5-(2-F... -

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Basic information

Entry
Database: PDB / ID: 6i47
TitleStructure of P. aeruginosa LpxC with compound 10: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-1-oxoisoindolin-2-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / : / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-UNY / Chem-UNZ / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSurivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. ...Surivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Enderlin-Paput, M. / Lange, R. / Bur, D. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Hermann, C. / Locher, H.H. / Seiler, P. / Mac Sweeney, A. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria.
Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. ...Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Herrmann, C. / Seiler, P. / Enderlin-Paput, M. / Mac Sweeney, A. / Wicki, M. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
History
DepositionNov 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1134
Polymers33,1471
Non-polymers9663
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.279, 66.503, 63.452
Angle α, β, γ (deg.)90.000, 90.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase / UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase


Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain LESB58) (bacteria)
Gene: lpxC, PLES_47851 / Production host: Escherichia coli (E. coli)
References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNY / (2~{R})-4-[6-(2-fluoranyl-4-methoxy-phenyl)-3-oxidanylidene-1~{H}-isoindol-2-yl]-2-methyl-2-methylsulfonyl-~{N}-oxidanyl-butanamide


Mass: 450.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FN2O6S
#4: Chemical ChemComp-UNZ / (2~{S})-4-[6-(2-fluoranyl-4-methoxy-phenyl)-3-oxidanylidene-1~{H}-isoindol-2-yl]-2-methyl-2-methylsulfonyl-~{N}-oxidanyl-butanamide


Mass: 450.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23FN2O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: obtained synthetically / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26-30% (w/v) PEG 4000, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.906 Å / Num. obs: 42579 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 1.86 % / CC1/2: 0.994 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→2.01 Å / Rmerge(I) obs: 0.732 / CC1/2: 0.405

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Processing

Software
NameVersionClassification
REFMAC5.8.0238 2018/15/10refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ves

2ves


Resolution: 1.9→45.906 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.18 / SU B: 5.969 / SU ML: 0.162 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2579 1185 -
Rwork0.2032 22518 -
all0.206 --
obs-23703 99.317 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.137 Å20 Å20.552 Å2
2---0.413 Å20 Å2
3----0.738 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 32 231 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172311
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.683378
X-RAY DIFFRACTIONr_angle_other_deg1.3171.65327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.7485.263323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83921.707123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87215404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9981518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.1920.2499
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22199
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21129
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21108
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2195
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.210
X-RAY DIFFRACTIONr_nbd_other0.1820.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.219
X-RAY DIFFRACTIONr_mcbond_it2.0652.8171237
X-RAY DIFFRACTIONr_mcbond_other2.0652.8151236
X-RAY DIFFRACTIONr_mcangle_it3.2744.221563
X-RAY DIFFRACTIONr_mcangle_other3.2774.2221560
X-RAY DIFFRACTIONr_scbond_it2.2653.0561245
X-RAY DIFFRACTIONr_scbond_other2.2643.0571246
X-RAY DIFFRACTIONr_scangle_it3.5684.4971814
X-RAY DIFFRACTIONr_scangle_other3.5674.4981815
X-RAY DIFFRACTIONr_lrange_it5.7133.2822797
X-RAY DIFFRACTIONr_lrange_other5.60933.0312752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.9-1.9490.407860.341624173498.61590.339
1.949-2.0030.325850.3051616171499.24150.304
2.003-2.0610.316810.2751550164799.02850.268
2.061-2.1240.282810.271543163999.08480.262
2.124-2.1930.327770.2411466155899.03720.228
2.193-2.270.283760.2381435152399.21210.221
2.27-2.3560.356720.2381385146299.6580.216
2.356-2.4510.297710.2181337141799.36490.195
2.451-2.560.321670.2011274134299.92550.179
2.56-2.6850.247640.211212128099.68750.182
2.685-2.8290.275610.2091172123499.9190.184
2.829-30.353590.2141116117699.9150.19
3-3.2060.294550.2021037109599.7260.185
3.206-3.4620.194510.203968102099.9020.193
3.462-3.790.231470.17990395599.47640.168
3.79-4.2340.19420.14879784998.82210.144
4.234-4.8820.197380.13972076499.21470.138
4.882-5.9630.193320.16161064599.53490.161
5.963-8.3620.207250.16147550898.42520.158
8.362-45.9060.154150.14927729897.98660.157

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