Research workbench
Crystal structure of the lpxc in complex with N-[(2S,3R)-3-hydroxy-1- (hydroxyamino)-1-oxobutan-2-YL]BIPHENYL-4-carboxamide inhibitor
Analyse Crystal structure of the lpxc in complex with N-[(2S,3R)-3-hydroxy-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FW7
- Type
- protein
- Length
- 1,206 residues
- Chains
- 4
- 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
- L63, ZN
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 301 | 25% helix, 32% strand | P47205 |
| C, D | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 302 | 25% helix, 33% strand | P47205 |
Ligands and binding sites
- L63 · N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]biphenyl-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 17 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.74 | 0.78 | 87 | empty |
| 2 | 809 | 0.72 | 0.78 | 78 | empty |
| 3 | 450 | 0.71 | 0.81 | 51 | L63 |
| 4 | 513 | 0.70 | 0.80 | 50 | ZN, L63 |
| 5 | 149 | 0.69 | 0.88 | 22 | GOL |
Interfaces
4 interfaces between chains.
- B–C · 541 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 533 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 282 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 256 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4FW7 · Crystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOB… · the same entry in another collection · chain B against B, 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 C 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 4FW7 · PDBe 4FW7 · UniProt P47205
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