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- PDB-3u1y: Potent Inhibitors of LpxC for the Treatment of Gram-Negative Infe... -

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Basic information

Entry
Database: PDB / ID: 3u1y
TitlePotent Inhibitors of LpxC for the Treatment of Gram-Negative Infections
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHydrolase/Hydrolase inhibitor / Pseudomonas aeruginosa / lpxc / gram negative / Hydrolase-Hydrolase inhibitor complex
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
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / 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 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-03I / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrown, M. / Abramite, J. / Liu, S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Potent inhibitors of LpxC for the treatment of Gram-negative infections.
Authors: Brown, M.F. / Reilly, U. / Abramite, J.A. / Arcari, J.T. / Oliver, R. / Barham, R.A. / Che, Y. / Chen, J.M. / Collantes, E.M. / Chung, S.W. / Desbonnet, C. / Doty, J. / Doroski, M. / ...Authors: Brown, M.F. / Reilly, U. / Abramite, J.A. / Arcari, J.T. / Oliver, R. / Barham, R.A. / Che, Y. / Chen, J.M. / Collantes, E.M. / Chung, S.W. / Desbonnet, C. / Doty, J. / Doroski, M. / Engtrakul, J.J. / Harris, T.M. / Huband, M. / Knafels, J.D. / Leach, K.L. / Liu, S. / Marfat, A. / Marra, A. / McElroy, E. / Melnick, M. / Menard, C.A. / Montgomery, J.I. / Mullins, L. / Noe, M.C. / O'Donnell, J. / Penzien, J. / Plummer, M.S. / Price, L.M. / Shanmugasundaram, V. / Thoma, C. / Uccello, D.P. / Warmus, J.S. / Wishka, D.G.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _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: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4717
Polymers66,2932
Non-polymers1,1775
Water5,621312
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7033
Polymers33,1471
Non-polymers5562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7684
Polymers33,1471
Non-polymers6213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules

A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4717
Polymers66,2932
Non-polymers1,1775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area610 Å2
ΔGint-39 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.995, 70.396, 219.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33146.617 Da / Num. of mol.: 2 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli (E. coli)
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-03I / (2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-{4'-[3-(morpholin-4-yl)propoxy]biphenyl-4-yl}butanamide


Mass: 490.612 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H34N2O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 39058 / Num. obs: 37925 / % possible obs: 0.971 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.93 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2VES

2ves


Resolution: 2→28.47 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9218 / SU R Cruickshank DPI: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1893 5.01 %RANDOM
Rwork0.1915 ---
obs0.1934 37790 97.16 %-
Displacement parametersBiso mean: 31.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.2148 Å20 Å20 Å2
2---6.1159 Å20 Å2
3---4.9011 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: LAST / Resolution: 2→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 71 312 5051
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014846HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1715SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes128HARMONIC2
X-RAY DIFFRACTIONt_gen_planes714HARMONIC5
X-RAY DIFFRACTIONt_it4846HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion16.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion623SEMIHARMONIC5
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_contact5683SEMIHARMONIC4
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2477 139 5.42 %
Rwork0.2364 2426 -
all0.237 2565 -
obs--0.972 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56530.1165-0.25880.7783-0.46361.4487-0.01210.034-0.0228-0.12310.03360.07950.120.0131-0.0215-0.08640.0005-0.0291-0.04470.0137-0.080710.98393.175141.7302
20.9188-0.0280.39050.57-0.21671.40730.0009-0.0547-0.049-0.04040.0001-0.03140.1341-0.0555-0.0011-0.05460.01330.0201-0.0490.015-0.074925.191336.558211.6877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|400 }A1 - 400
2X-RAY DIFFRACTION2{ B|1 - B|400 }B1 - 400

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