Crystal structure of the lpxc in complex with N-[(2S)-3-amino-1- (hydroxyamino)-1-oxopropan-2-yl]-4-(4-phenylbuta-1,3-diyn-1-yl) benzamide inhibitor

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).

Ligands and binding sites

• L52 · N-[(2S)-3-amino-1-(hydroxyamino)-1-oxopropan-2-yl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide · ligand · 4 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 2 copies · chains A, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–C · 454 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 449 Ų buried · 13 hydrogen bonds · protein-protein
• A–D · 233 Ų buried · 2 hydrogen bonds · protein-protein
• B–D · 170 Ų buried · 2 hydrogen bonds · protein-protein
• C–D · 25 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 4FW3 · Crystal Structure of the LpxC in complex with N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN… · the same entry in another collection · chain A against A, TM-score 1.00
• P47205 · AlphaFold monomer V2.0 prediction for udp-3-O-acyl-N- acetylglucosamine deacetylase… · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P47205
• Elsewhere: RCSB PDB 4FW3 · PDBe 4FW3 · UniProt P47205