MolNFT v1 · #129661 · protein
Xiap in complex with small molecule
5OQW · E3 ubiquitin-protein ligase xiap: “Xiap in complex with small molecule”. X-ray diffraction, 3 ligands (A4E, ZN, NA), 2 pockets (best druggability 0.56). MolNFT v1 #129661 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OQW
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap
- EC
- 2.3.2.27
- UniProt
- P98170
- Ligands
- A4E, ZN, NA
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 106 | 45% helix, 8% strand | P98170 |
| B | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 107 | 44% helix, 7% strand | P98170 |
Ligands and binding sites
- A4E · 1-[6-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-[(2~{R}, 5~{R})-5-methyl-2-[[(3~{R})-3-methylmorpholin-4-yl]methyl]piperazin-4-ium-1-yl]ethanone · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.56 | 0.88 | 18 | empty |
| 2 | 149 | 0.46 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 933 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5OQW · XIAP in complex with small molecule · the same entry in another collection · 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 P98170
- Elsewhere: RCSB PDB 5OQW · PDBe 5OQW · UniProt P98170
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