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- PDB-6i49: Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy... -

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Basic information

Entry
Database: PDB / ID: 6i49
TitleStructure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy-2-methyl-2-(methylsulfonyl)-4(6((4(morpholinomethyl)phenyl)ethynyl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)yl)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-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / 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-H2Z / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
BBB: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4536
Polymers66,2932
Non-polymers1,1604
Water3,027168
1
AAA: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7273
Polymers33,1471
Non-polymers5802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7273
Polymers33,1471
Non-polymers5802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.313, 89.178, 35.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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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.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-H2Z / (2~{R})-2-methyl-2-methylsulfonyl-4-[6-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]-3-oxidanylidene-1~{H}-pyrrolo[1,2-c]imidazol-2-yl]-~{N}-oxidanyl-butanamide


Mass: 514.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30N4O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate pH 4.6, 7 % (w/v) PEG 400, 7 % (w/v) PEG 500 MME, 7 % (w/v) PEG 600, 7 % (w/v) PEG 1000, 5 % (v/v) ethylene glycol

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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-F / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→43.122 Å / Num. obs: 74154 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.7
Reflection shellResolution: 1.94→2.06 Å / Mean I/σ(I) obs: 2.1 / CC1/2: 0.725 / % possible all: 96.4

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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: 1.94→43.122 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.595 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2429 1982 -
Rwork0.1832 --
all0.186 --
obs-39617 98.186 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.851 Å20 Å20 Å2
2--0.025 Å2-0 Å2
3----0.877 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4545 0 68 168 4781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0134757
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174441
X-RAY DIFFRACTIONr_angle_refined_deg2.4171.6156461
X-RAY DIFFRACTIONr_angle_other_deg1.6191.56310219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4175609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55721.765238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6781534
X-RAY DIFFRACTIONr_chiral_restr0.1110.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021033
X-RAY DIFFRACTIONr_nbd_refined0.2190.2930
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.24579
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22417
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.223
X-RAY DIFFRACTIONr_nbd_other0.230.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2080.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_mcbond_it3.1852.3822415
X-RAY DIFFRACTIONr_mcbond_other3.1712.3812414
X-RAY DIFFRACTIONr_mcangle_it3.933.5553027
X-RAY DIFFRACTIONr_mcangle_other3.9293.5553028
X-RAY DIFFRACTIONr_scbond_it4.4182.7862342
X-RAY DIFFRACTIONr_scbond_other4.4172.7882343
X-RAY DIFFRACTIONr_scangle_it6.1154.0253432
X-RAY DIFFRACTIONr_scangle_other6.1144.0273433
X-RAY DIFFRACTIONr_lrange_it6.86928.5885209
X-RAY DIFFRACTIONr_lrange_other6.89828.5515188
X-RAY DIFFRACTIONr_ncsr_local_group_10.120.059053
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
1.94-1.990.3071410.2422669295095.25420.225
1.99-2.0450.2861400.2122653282498.90230.192
2.045-2.1040.3121330.222538278296.01010.198
2.104-2.1690.2341340.2022547268999.70250.179
2.169-2.240.2541270.1992409263796.16990.174
2.24-2.3180.2691250.1922378250999.76090.163
2.318-2.4050.2531200.1782271246996.84080.152
2.405-2.5030.2531170.1922233237598.94740.161
2.503-2.6140.2491110.192098225298.09060.159
2.614-2.7410.2821090.2012067222197.97390.169
2.741-2.8890.291020.1781951205699.85410.151
2.889-3.0630.223970.1771838197298.12370.154
3.063-3.2740.251920.1961743186198.60290.175
3.274-3.5340.221870.1841651175299.20090.169
3.534-3.8690.25800.1781524161299.50370.167
3.869-4.3220.211720.1521375145999.17750.144
4.322-4.9830.191660.1351244131999.31770.133
4.983-6.0840.235560.1771061112699.20070.168
6.084-8.5250.207450.17285289999.77750.169
8.525-44.5890.188280.18453356998.5940.195

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