MolNFT v1 · #155942 · protein
Crystal structure of eed in complex with EZH2 peptide and compound 11#
6LO2 · Polycomb protein eed: “Crystal structure of eed in complex with EZH2 peptide and compound 11#”. X-ray diffraction, 1 ligand (EJU), 9 pockets (best druggability 0.87). MolNFT v1 #155942 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6LO2
- 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
- UniProt
- O75530, Q15910
- Ligands
- EJU
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb protein eed | protein | 364 | 3% helix, 45% strand | O75530 |
| B | Polycomb protein eed | protein | 357 | 3% helix, 47% strand | O75530 |
| C, D | Histone-lysine N-methyltransferase EZH2 | protein | 29 | 72% helix, 0% strand | Q15910 |
Ligands and binding sites
- EJU · 8-[4-[(dimethylamino)methyl]phenyl]-N-[(2-methoxyphenyl)methyl]-[1,2,4]triazolo[4,3-a]pyridin-5-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.87 | 0.94 | 42 | empty |
| 2 | 424 | 0.86 | 0.93 | 42 | empty |
| 3 | 108 | 0.59 | 0.86 | 19 | empty |
| 4 | 71 | 0.58 | 0.89 | 13 | EJU |
| 5 | 62 | 0.57 | 0.89 | 11 | EJU |
Interfaces
3 interfaces between chains.
- A–C · 1532 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1515 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LO2 · Crystal structure of EED in complex with EZH2 peptide and 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 B 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 6LO2 · PDBe 6LO2 · UniProt O75530 · UniProt Q15910
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