Research workbench
Lpxc from P.AERUGINOSA with the inhibitor 6-(benzimidazol-1-yl)-5-[4- [2-[6-[(4-methylpiperazin-1-YL)METHYL]-3- PYRIDYL]ETHYNYL]PHENYL]PYRIDINE-3-carbohydroxamic acid
Analyse Lpxc from P.AERUGINOSA with the inhibitor 6-(benzimidazol-1-yl)-5-[4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OKG
- Type
- protein
- Length
- 590 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- P47205
- Ligands
- 2SZ, ZN
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 299 | 24% helix, 37% strand | P47205 |
| B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 291 | 25% helix, 34% strand | P47205 |
Ligands and binding sites
- 2SZ · 6-(1H-benzimidazol-1-yl)-N-hydroxy-5-[4-({6-[(4-methylpiperazin-1-yl)methyl]pyridin-3-yl}ethynyl)phenyl]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.68 | 0.88 | 27 | empty |
| 2 | 144 | 0.68 | 0.88 | 22 | empty |
| 3 | 424 | 0.68 | 0.80 | 44 | ZN, 2SZ |
| 4 | 380 | 0.67 | 0.80 | 40 | 2SZ |
| 5 | 100 | 0.52 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 787 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4OKG · LpxC from P.aeruginosa with the inhibitor 6-(benzimidazol-1-yl)-5-[4-[2-[6-[(4-methylpiper… · 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 B 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 4OKG · PDBe 4OKG · UniProt P47205
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