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- PDB-29ah: Crystal structure of PaLpxC complexed with compound 6 -

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Basic information

Entry
Database: PDB / ID: 29ah
TitleCrystal structure of PaLpxC complexed with compound 6
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: 2.2 Å
AuthorsBeaumont, E.J. / 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)33,7033
Polymers33,1471
Non-polymers5562
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13150 Å2
Unit cell
Length a, b, c (Å)35.591, 79.096, 50.745
Angle α, β, γ (deg.)90.00, 92.30, 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: 33146.617 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-A1J1T / 4-[(2~{R})-1-(2-fluoranylethylamino)-3-[4-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]phenyl]propan-2-yl]-5-oxidanyl-1~{H}-pyrimidin-6-one


Mass: 490.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31FN4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane pH6.5, 0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.2→42.7 Å / Num. obs: 10819 / % possible obs: 78.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 24.86 Å2 / Rrim(I) all: 0.14 / Net I/σ(I): 5.3
Reflection shellResolution: 2.2→2.34 Å / Num. unique obs: 541 / CC1/2: 0.63

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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: 2.2→42.69 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.88 / SU R Cruickshank DPI: 0.716 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.605 / SU Rfree Blow DPI: 0.291 / SU Rfree Cruickshank DPI: 0.3
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 494 4.57 %RANDOM
Rwork0.2017 ---
obs0.2046 10819 75.5 %-
Displacement parametersBiso mean: 23.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.574 Å20 Å2-0.3652 Å2
2--0.1658 Å20 Å2
3---0.4081 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 37 58 2396
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082411HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.663289HARMONIC4
X-RAY DIFFRACTIONt_dihedral_angle_d846SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes423HARMONIC5
X-RAY DIFFRACTIONt_it2379HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion16.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion307SEMIHARMONIC5
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_contact1884SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.3284 -3.99 %
Rwork0.2799 433 -
all0.282 451 -
obs--20.99 %
Refinement TLS params.Method: refined / Origin x: 7.2162 Å / Origin y: -0.9604 Å / Origin z: 14.3847 Å
111213212223313233
T-0.056 Å20.0103 Å2-0.0337 Å2--0.0549 Å20.0002 Å2---0.0035 Å2
L0.8766 °20.1815 °2-0.0577 °2-1.0034 °2-0.099 °2--0.3413 °2
S0.0219 Å °0.0572 Å °-0.0117 Å °-0.0063 Å °-0.0042 Å °0.0252 Å °0.0134 Å °0.0335 Å °-0.0177 Å °
Refinement TLS groupSelection details: { A|* }

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