MolNFT v1 · #138321 · protein
Humanized mutant of the chaetomium thermophilum polycomb repressive complex 2 bound to the inhibitor GSK126
5WFD · Polycomb protein eed: “Humanized mutant of the chaetomium thermophilum polycomb repressive complex 2 bound to the inhibitor GSK126”. X-ray diffraction, 2 ligands (A9G, ZN), 17 pockets (best druggability 0.85). MolNFT v1 #138321 on…
- PDB
- 5WFD
- Type
- protein
- Length
- 1,240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed; Histone-lysine-N-methyltransferase EZH2, polycomb protein SUZ12…
- UniProt
- G0S8H7, G0SDW4, G0RYC6
- Ligands
- A9G, ZN
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 466 | 10% helix, 40% strand | G0S8H7 |
| B | Histone-lysine-N-methyltransferase EZH2, polycomb protein SUZ12 chimera | protein | 774 | 37% helix, 12% strand | G0SDW4, G0RYC6 |
Ligands and binding sites
- A9G · 1-[(2S)-butan-2-yl]-N-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indole-4-carboxamide · ligand · chains B
- ZN · Zinc ion · metal · 8 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.85 | 0.88 | 78 | empty |
| 2 | 685 | 0.81 | 0.86 | 73 | empty |
| 3 | 396 | 0.79 | 0.88 | 56 | empty |
| 4 | 787 | 0.78 | 0.81 | 96 | empty |
| 5 | 907 | 0.72 | 0.76 | 78 | empty |
Interfaces
1 interface between chains.
- A–B · 5325 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 5WFD · Humanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to… · 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 G0S8H7
- Every structure of UniProt G0SDW4
- Every structure of UniProt G0RYC6
- Elsewhere: RCSB PDB 5WFD · PDBe 5WFD · UniProt G0S8H7 · UniProt G0SDW4 · UniProt G0RYC6
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