MolNFT v1 · #120463 · protein
Eed in complex with PRC2 allosteric inhibitor EED210
5H17 · Polycomb protein eed: “Eed in complex with PRC2 allosteric inhibitor EED210”. X-ray diffraction, 1 ligand (LQE), 5 pockets (best druggability 0.86). MolNFT v1 #120463 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H17
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb protein eed; Histone-lysine N-methyltransferase EZH2
- EC
- 2.1.1.43
- UniProt
- O75530, Q15910
- Ligands
- LQE
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 357 | 3% helix, 47% strand | O75530 |
| B | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 27 | 81% helix, 0% strand | Q15910 |
Ligands and binding sites
- LQE · (3R,4aS,10aS)-6-methoxy-3-[(3-methoxyphenyl)methyl]-1-methyl-3,4,4a,5,10,10a-hexahydro-2H-benzo[g]quinoline · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.86 | 0.93 | 41 | empty |
| 2 | 101 | 0.60 | 0.87 | 18 | empty |
| 3 | 95 | 0.55 | 0.84 | 14 | LQE |
| 4 | 127 | 0.49 | 0.79 | 22 | empty |
| 5 | 50 | 0.33 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1221 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5H17 · EED in complex with PRC2 allosteric inhibitor EED210 · the same entry in another collection · chain A against A, TM-score 1.00
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q15910 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EZH2 (Q15910) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 O75530
- Every structure of UniProt Q15910
- Elsewhere: RCSB PDB 5H17 · PDBe 5H17 · UniProt O75530 · UniProt Q15910
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.