MolNFT v1 · #120495 · protein
Eed in complex with PRC2 allosteric inhibitor compound 11
5H25 · Polycomb protein eed: “Eed in complex with PRC2 allosteric inhibitor compound 11”. X-ray diffraction, 1 ligand (LQH), 8 pockets (best druggability 0.86). MolNFT v1 #120495 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5H25
- Type
- protein
- Length
- 779 residues
- Chains
- 4
- 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
- LQH
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 364 | 4% helix, 46% strand | O75530 |
| B | Polycomb protein eed | protein | 357 | 3% helix, 47% strand | O75530 |
| C, D | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 29 | 72% helix, 0% strand | Q15910 |
Ligands and binding sites
- LQH · 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.86 | 0.94 | 46 | empty |
| 2 | 385 | 0.86 | 0.94 | 46 | empty |
| 3 | 92 | 0.60 | 0.87 | 20 | empty |
| 4 | 85 | 0.54 | 0.85 | 20 | empty |
| 5 | 53 | 0.48 | 0.86 | 14 | LQH |
Interfaces
4 interfaces between chains.
- B–D · 1549 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1521 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 17 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H25 · EED in complex with PRC2 allosteric inhibitor compound 11 · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.86
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 5H25 · PDBe 5H25 · UniProt O75530 · UniProt Q15910
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.