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- PDB-29ai: Crystal structure of EcLpxC complexed with compound 7a -

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Basic information

Entry
Database: PDB / ID: 29ai
TitleCrystal structure of EcLpxC complexed with compound 7a
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 / metal ion binding / membrane
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.618 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
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
C: UDP-3-O-acyl-N-acetylglucosamine deacetylase
D: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,36816
Polymers130,0604
Non-polymers2,30812
Water724
1
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0924
Polymers32,5151
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0924
Polymers32,5151
Non-polymers5773
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0924
Polymers32,5151
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0924
Polymers32,5151
Non-polymers5773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.661, 146.742, 99.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 32515.107 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxC, EcE24377A_0098 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A7ZHI7, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-A1J1S / 5-oxidanyl-4-[2-[4-[2-[4-[[(3-oxidanylcyclobutyl)amino]methyl]phenyl]ethynyl]phenyl]ethyl]-1~{H}-pyrimidin-6-one


Mass: 415.484 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H25N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Phosphate/citrate pH 4.2, 0.2 M Li2SO4 and 20% w/v PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.618→82.48 Å / Num. obs: 27030 / % possible obs: 92.3 % / Redundancy: 6.4 % / CC1/2: 0.813 / Net I/σ(I): 4.5
Reflection shellResolution: 2.62→2.93 Å / Num. unique obs: 1351 / CC1/2: 0.6 / Rrim(I) all: 1.98 / % possible all: 51.4

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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: 2.618→31.25 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.462
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1375 5.1 %RANDOM
Rwork0.2448 ---
obs0.2462 26974 65.5 %-
Displacement parametersBiso mean: 36.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.8314 Å20 Å20 Å2
2---1.9195 Å20 Å2
3---1.0881 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.618→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 148 4 9228
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079505HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.5812953HARMONIC4
X-RAY DIFFRACTIONt_dihedral_angle_d3299SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1679HARMONIC5
X-RAY DIFFRACTIONt_it9405HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion16.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1212SEMIHARMONIC5
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_contact6807SEMIHARMONIC4
LS refinement shellResolution: 2.62→2.81 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.347 -4.81 %
Rwork0.344 514 -
all0.3442 540 -
obs--6.85 %
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)
11.16520.6564-0.13911.96540.84552.5480.08860.0037-0.0168-0.0057-0.03720.04450.0756-0.0049-0.0514-0.1754-0.0153-0.0119-0.0652-0.0203-0.027119.6327.281441.9738
21.3456-0.46750.35962.43190.38212.58120.0664-0.1066-0.0328-0.2996-0.0298-0.0133-0.27310.0162-0.0367-0.0049-0.0162-0.0208-0.14860.0149-0.118619.599511.52768.0776
30.79180.3901-0.09512.9888-1.91753.27310.3008-0.015-0.26430.5216-0.2462-0.1389-0.3664-0.0702-0.05460.186-0.0757-0.0949-0.28150.0574-0.254823.420264.892820.2688
41.19740.0723-0.0022.12530.91862.19680.07520.0675-0.0349-0.1154-0.1440.0898-0.23770.02540.0688-0.11050.03780.0097-0.085-0.0486-0.0412-23.036626.238529.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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