PDB-10ry: Crystal structure of compound 8t bound to PaLpxC

ID or keywords:

Entry

Database: PDB / ID: 10ry

Title

Crystal structure of compound 8t bound to PaLpxC

Components

UDP-3-O-acyl-N-acetylglucosamine deacetylase

Keywords

HYDROLASE / Inhibitor complex

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 / membrane / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.902 Å

Authors

Martin, D.P.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Feb 4, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10ry.cif.gz	82 KB	Display	PDBx/mmCIF format
PDB format	pdb10ry.ent.gz		Display	PDB format
PDBx/mmJSON format	10ry.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/0r/10ry ftp://data.pdbj.org/pub/pdb/validation_reports/0r/10ry	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UDP-3-O-acyl-N-acetylglucosamine deacetylase

hetero molecules

34 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	108.745, 108.745, 58.261
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-641- HOH

#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: 33375.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-A1C8O / 1-{(2S)-3-(5-hydroxy-6-oxo-1,6-dihydropyrimidin-4-yl)-2-[4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)phenyl]propyl}azetidine-3-carbonitrile Mass: 509.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃₀H₃₁N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris pH 7.4, 32% PEG Smear Medium, 2% glycerol, 2 mM TCEP

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
Detector	Type: APEX II CCD / Detector: CCD / Date: Aug 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5406 Å / Relative weight: 1
Reflection	Resolution: 1.9→36.62 Å / Num. obs: 31043 / % possible obs: 100 % / Redundancy: 1.9 % / CC_1/2: 0.999 / Χ²: 0.98 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.902→1.951 Å / Redundancy: 1.8 % / Num. unique obs: 324 / CC_1/2: 1 / Χ²: 0.43 / % possible all: 98.7

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Processing

Software

Name: REFMAC / Version: 5.8.0430 (refmacat 0.4.126) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.902→35.621 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.938 / SU B: 3.463 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2299	1606	5.176 %
R_work	0.1979	29420	-
all	0.2	-	-
obs	-	31026	99.942 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.624 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.532 Å²	0.266 Å²	0 Å²
2-	-	0.532 Å²	-0 Å²
3-	-	-	-1.725 Å²

Refinement step

Cycle: LAST / Resolution: 1.902→35.621 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2348	0	44	157	2549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2440
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2347
X-RAY DIFFRACTION	r_angle_refined_deg	1.763	1.825	3300
X-RAY DIFFRACTION	r_angle_other_deg	0.598	1.759	5394
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.035	5	303
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.806	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.609	10	418
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.939	10	111
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	376
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2862
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	563
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	436
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	2167
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1205
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1364
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	125
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.198	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.141	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.215	0.2	17
X-RAY DIFFRACTION	r_mcbond_it	3.049	2.787	1209
X-RAY DIFFRACTION	r_mcbond_other	3.048	2.787	1209
X-RAY DIFFRACTION	r_mcangle_it	4.646	4.984	1510
X-RAY DIFFRACTION	r_mcangle_other	4.644	4.988	1511
X-RAY DIFFRACTION	r_scbond_it	4.252	3.409	1231
X-RAY DIFFRACTION	r_scbond_other	4.246	3.398	1228
X-RAY DIFFRACTION	r_scangle_it	6.546	6.002	1787
X-RAY DIFFRACTION	r_scangle_other	6.551	5.981	1782
X-RAY DIFFRACTION	r_lrange_it	8.989	29.076	2644
X-RAY DIFFRACTION	r_lrange_other	8.985	27.914	2606

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.902-1.951	0.278	120	0.262	2167	0.263	2296	0.952	0.95	99.608	0.256
1.951-2.004	0.268	106	0.245	2090	0.246	2196	0.953	0.958	100	0.234
2.004-2.062	0.305	109	0.239	2040	0.243	2149	0.929	0.961	100	0.225
2.062-2.125	0.272	126	0.225	2001	0.227	2127	0.953	0.966	100	0.209
2.125-2.195	0.257	121	0.226	1887	0.228	2008	0.952	0.965	100	0.205
2.195-2.272	0.249	115	0.213	1862	0.215	1977	0.963	0.97	100	0.196
2.272-2.357	0.255	121	0.218	1768	0.22	1889	0.958	0.97	100	0.192
2.357-2.453	0.236	93	0.218	1750	0.219	1843	0.964	0.97	100	0.193
2.453-2.561	0.222	71	0.228	1679	0.228	1750	0.97	0.969	100	0.2
2.561-2.686	0.248	67	0.217	1600	0.219	1667	0.966	0.97	100	0.189
2.686-2.83	0.271	84	0.206	1516	0.21	1600	0.954	0.974	100	0.186
2.83-3.001	0.256	58	0.212	1469	0.214	1527	0.963	0.971	100	0.199
3.001-3.206	0.265	84	0.208	1343	0.212	1428	0.96	0.972	99.93	0.202
3.206-3.461	0.265	67	0.214	1273	0.217	1341	0.961	0.972	99.9254	0.213
3.461-3.787	0.218	62	0.199	1158	0.2	1220	0.98	0.979	100	0.204
3.787-4.228	0.182	62	0.158	1051	0.159	1115	0.98	0.984	99.8206	0.177
4.228-4.871	0.139	47	0.128	945	0.128	992	0.989	0.989	100	0.151
4.871-5.938	0.191	38	0.165	804	0.167	842	0.98	0.985	100	0.194
5.938-8.284	0.179	33	0.164	640	0.165	673	0.982	0.982	100	0.197
8.284-35.621	0.164	22	0.157	376	0.157	398	0.981	0.983	100	0.202

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