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- PDB-29ak: Crystal structure of PaLpxC complexed with compound 8k -

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Basic information

Entry
Database: PDB / ID: 29ak
TitleCrystal structure of PaLpxC complexed with compound 8k
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsANTIBIOTIC / LpxC / metalloprotease / 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
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
: / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 Å
AuthorsBeaumont, E. / Cade, I. / Kopec, J. / Martin, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Discovery and Optimization of Novel Nonhydroxamate LpxC Inhibitors for the Treatment of Multidrug-Resistant Gram-Negative Infections.
Authors: Martin, D.P. / Teng, M. / Nammalwar, B. / Perez, C. / Li, X. / Munguia, J. / Taganov, K. / Fan, J. / Agarwalla, S. / Lonergan, D. / Tomaras, A.P. / Zimmerman, Z. / Puerta, D.T.
History
DepositionMar 3, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,9285
Polymers33,2341
Non-polymers6944
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.961, 66.807, 64.212
Angle α, β, γ (deg.)90.00, 90.53, 90.00
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: 33233.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lpxC, envA, PA4406 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P47205, 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-A1J1V / 4-[(2S)-3-[[(2S)-1-fluoranylpropan-2-yl]amino]-2-[4-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]phenyl]propyl]-5-oxidanyl-1H-pyrimidin-6-one


Mass: 504.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33FN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane pH8.5, 0.2 M ammonium nitrate, 18 % v/v PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→64.21 Å / Num. obs: 31928 / % possible obs: 72.2 % / Redundancy: 3 % / Biso Wilson estimate: 15.71 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 1.5→1.64 Å / Num. unique obs: 1596 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (22-FEB-2023)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.504→64.21 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.123
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1507 4.72 %RANDOM
Rwork0.1853 ---
obs0.1879 31928 66.1 %-
Displacement parametersBiso mean: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.196 Å20 Å2-0.2294 Å2
2---1.5491 Å20 Å2
3---3.7451 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.504→64.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 46 296 2682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012588HARMONIC4
X-RAY DIFFRACTIONt_angle_deg0.933565HARMONIC4
X-RAY DIFFRACTIONt_dihedral_angle_d944SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it2543HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.02
X-RAY DIFFRACTIONt_other_torsion15.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion335SEMIHARMONIC5
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_contact2643SEMIHARMONIC4
LS refinement shellResolution: 1.504→1.59 Å
RfactorNum. reflection% reflection
Rfree0.3071 -4.38 %
Rwork0.2658 611 -
obs--8.75 %
Refinement TLS params.Method: refined / Origin x: 6.78 Å / Origin y: -4.841 Å / Origin z: 18.7611 Å
111213212223313233
T-0.0486 Å20.0048 Å20.0055 Å2--0.0272 Å2-0.0053 Å2--0.0385 Å2
L0.2577 °20.0604 °20.1691 °2-0.4041 °2-0.0683 °2--0.1615 °2
S0.0098 Å °0.0042 Å °0.0068 Å °-0.0687 Å °0.0027 Å °-0.024 Å °0.0014 Å °0.0051 Å °-0.0124 Å °
Refinement TLS groupSelection details: { A|* }

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