MolNFT v1 · #120461 · protein
Eed in complex with PRC2 allosteric inhibitor EED709
5H15 · Polycomb protein eed: “Eed in complex with PRC2 allosteric inhibitor EED709”. X-ray diffraction, 1 ligand (LQD), 8 pockets (best druggability 0.86). MolNFT v1 #120461 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5H15
- Type
- protein
- Length
- 778 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
- LQD
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 356 | 3% helix, 46% strand | O75530 |
| B | Polycomb protein eed | protein | 364 | 3% helix, 46% strand | O75530 |
| C, D | Histone-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 29 | 76% helix, 0% strand | Q15910 |
Ligands and binding sites
- LQD · (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.86 | 0.94 | 41 | empty |
| 2 | 413 | 0.85 | 0.93 | 41 | empty |
| 3 | 101 | 0.62 | 0.87 | 18 | empty |
| 4 | 89 | 0.59 | 0.87 | 18 | empty |
| 5 | 108 | 0.54 | 0.83 | 13 | LQD |
Interfaces
5 interfaces between chains.
- A–C · 1509 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1482 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 52 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H15 · EED in complex with PRC2 allosteric inhibitor EED709 · 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 D against A, TM-score 0.85
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 5H15 · PDBe 5H15 · UniProt O75530 · UniProt Q15910
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