Crystal structure of the lpxc in complex with N-[(2S,3R)-3-hydroxy-1- (hydroxyamino)-1-oxobutan-2-yl]-4-(PHENYLETHYNYL)BENZAMIDE inhibitor

Structure

x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).

Ligands and binding sites

• L59 · N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide · ligand · 4 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
• NA · Sodium ion · metal · chains D
• GOL · Glycerol · additive · 9 copies · chains A, B, C, D
• ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
• PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B

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

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• B–D · 523 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 495 Ų buried · 8 hydrogen bonds · protein-protein
• A–B · 413 Ų buried · 9 hydrogen bonds · protein-protein
• A–D · 192 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 187 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 4FW6 · Crystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOB… · 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 4FW6 · PDBe 4FW6 · UniProt P47205