MolNFT v1 · #92069 · protein
Crystal structure of the lpxc in complex with N-[(1S,2R)-2-hydroxy-1- (HYDROXYCARBAMOYL)PROPYL]-4-(4-phenylbuta-1,3-diyn-1-YL)BENZAMIDE inhibitor
4FW4 · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Crystal structure of the lpxc in complex with N-[(1S,2R)-2-hydroxy-1…”. X-ray diffraction, 2 ligands (3P3, ZN), 16 pockets (best druggability 0.76). MolNFT v1 #92069 on…
- PDB
- 4FW4
- Type
- protein
- Length
- 1,204 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
- 3P3, ZN
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 300 | 25% helix, 32% strand | P47205 |
| C, D | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 302 | 24% helix, 32% strand | P47205 |
Ligands and binding sites
- 3P3 · N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-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 · 3 copies · chains B, C, D
- ACT · Acetate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.76 | 0.80 | 88 | ZN, 3P3 |
| 2 | 324 | 0.69 | 0.83 | 42 | 3P3 |
| 3 | 358 | 0.69 | 0.82 | 43 | 3P3 |
| 4 | 156 | 0.68 | 0.88 | 24 | GOL |
| 5 | 146 | 0.66 | 0.87 | 26 | GOL |
Interfaces
5 interfaces between chains.
- B–D · 539 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 530 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 384 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4FW4 · Crystal Structure of the LpxC in complex with N-[(1S,2R)-2-HYDROXY-1-(HYDROXYCARBAMOYL)PRO… · 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 4FW4 · PDBe 4FW4 · UniProt P47205
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