MolNFT v1 · #120465 · protein
Eed in complex with PRC2 allosteric inhibitor EED162
5H19 · Polycomb protein eed: “Eed in complex with PRC2 allosteric inhibitor EED162”. X-ray diffraction, 1 ligand (LQF), 3 pockets (best druggability 0.87). MolNFT v1 #120465 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H19
- 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
- LQF
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 355 | 3% helix, 48% strand | O75530 |
| B | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 29 | 72% helix, 0% strand | Q15910 |
Ligands and binding sites
- LQF · 5-(furan-2-ylmethylamino)-9-(phenylmethyl)-8,10-dihydro-7H-[1,2,4]triazolo[3,4-a][2,7]naphthyridine-6-carbonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.87 | 0.94 | 41 | empty |
| 2 | 60 | 0.54 | 0.88 | 10 | LQF |
| 3 | 51 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1555 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5H19 · EED in complex with PRC2 allosteric inhibitor EED162 · 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 1.00
- 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 0.87
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 5H19 · PDBe 5H19 · UniProt O75530 · UniProt Q15910
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