Research workbench
Lpxc from A.AAEOLICUS in complex with 4-[[4-[2-[4-(morpholinomethyl) PHENYL]ETHYNYL]PHENOXY]METHYL]TETRAHYDROPYRAN-4-carbohydroxamic acid (compound 9)
Analyse Lpxc from A.AAEOLICUS in complex with 4-[[4-[2-[4-(morpholinomethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U3D
- Type
- protein
- Length
- 267 residues
- Chains
- 1
- 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
- O67648
- Ligands
- 3BX, ZN, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 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 | 267 | 24% helix, 35% strand | O67648 |
Ligands and binding sites
- 3BX · N-hydroxy-4-[(4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}phenoxy)methyl]tetrahydro-2H-pyran-4-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.72 | 0.82 | 43 | ZN, 3BX |
Compared structures
- 4U3D · LpxC from A.Aaeolicus in complex with 4-[[4-[2-[4-(morpholinomethyl)phenyl]ethynyl]phenoxy… · the same entry in another collection · chain A against A, TM-score 1.00
- O67648 · 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 1.00
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 O67648
- Elsewhere: RCSB PDB 4U3D · PDBe 4U3D · UniProt O67648
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