MolNFT v1 · #126079 · protein
Structure of human polycomb repressive complex 2 (PRC2) with inhibitor
5LS6 · Histone-lysine N-methyltransferase EZH2,HISTONE-lysine N…: “Structure of human polycomb repressive complex 2 (PRC2) with inhibitor”. X-ray diffraction, 2 ligands (74D, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #126079 on…
- PDB
- 5LS6
- Type
- protein
- Length
- 4,282 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EZH2,HISTONE-lysine N- methyltransferase…
- EC
- 2.1.1.43
- UniProt
- Q15910, O75530, Q15022
- Ligands
- 74D, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, J | Histone-lysine N-methyltransferase EZH2,HISTONE-lysine N- methyltransferase EZH2,HISTONE-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 570 | 32% helix, 13% strand | Q15910 |
| B, E, H, K | Polycomb protein eed | protein | 365 | 4% helix, 46% strand | O75530 |
| C, F, I, L | Polycomb protein SUZ12 | protein | 125 | 62% helix, 2% strand | Q15022 |
| G | Histone-lysine N-methyltransferase EZH2,HISTONE-lysine N- methyltransferase EZH2,HISTONE-lysine N-methyltransferase EZH2 (EC 2.1.1.43) | protein | 572 | 31% helix, 14% strand | Q15910 |
| Q, R, S, T | JARID2 K116ME3 | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- 74D · 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide · ligand · 4 copies · chains A, B, D, E, G, H, J, K
- ZN · Zinc ion · metal · 32 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.87 | 0.94 | 37 | empty |
| 2 | 447 | 0.87 | 0.94 | 36 | empty |
| 3 | 423 | 0.87 | 0.95 | 40 | empty |
| 4 | 388 | 0.86 | 0.95 | 40 | empty |
| 5 | 1031 | 0.85 | 0.86 | 125 | empty |
Interfaces
33 interfaces between chains.
- A–B · 4439 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 4428 Ų buried · 57 hydrogen bonds · protein-protein
- G–H · 4331 Ų buried · 59 hydrogen bonds · protein-protein
- J–K · 4321 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 3122 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 5LS6 · Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor · the same entry in another collection · chain K against K, TM-score 1.00
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 Q15910
- Every structure of UniProt O75530
- Every structure of UniProt Q15022
- Elsewhere: RCSB PDB 5LS6 · PDBe 5LS6 · UniProt Q15910 · UniProt O75530 · UniProt Q15022
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