MolNFT v1 · #122239 · protein
Structure of the primary oncogenic mutant Y641N HS/ACPRC2 in complex with a pyridone inhibitor
5IJ8 · Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N…: “Structure of the primary oncogenic mutant Y641N HS/ACPRC2 in complex with a pyridone inhibitor”. X-ray diffraction, 2 ligands (6BN, ZN), 20 pockets (best druggability 0.87).…
- PDB
- 5IJ8
- Type
- protein
- Length
- 1,903 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N- methyltransferase EZH2; Polycomb…
- EC
- 2.1.1.43
- UniProt
- G1KPH4, Q15910, O75530, Q15022
- Ligands
- 6BN, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N- methyltransferase EZH2 (EC 2.1.1.43) | protein | 464 | 34% helix, 17% strand | G1KPH4, Q15910 |
| B | Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N- methyltransferase EZH2 (EC 2.1.1.43) | protein | 466 | 35% helix, 17% strand | G1KPH4, Q15910 |
| E | Polycomb protein eed | protein | 358 | 5% helix, 48% strand | O75530 |
| F | Polycomb protein eed | protein | 359 | 5% helix, 48% strand | O75530 |
| S, T | Polycomb protein SUZ12 | protein | 128 | 63% helix, 2% strand | Q15022 |
Ligands and binding sites
- 6BN · 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one · ligand · 2 copies · chains A, F, B, E
- ZN · Zinc ion · metal · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.87 | 0.94 | 45 | empty |
| 2 | 450 | 0.87 | 0.94 | 42 | empty |
| 3 | 665 | 0.85 | 0.89 | 94 | empty |
| 4 | 483 | 0.84 | 0.90 | 68 | empty |
| 5 | 906 | 0.77 | 0.80 | 95 | empty |
Interfaces
8 interfaces between chains.
- A–F · 3562 Ų buried · 52 hydrogen bonds · protein-protein
- B–E · 3499 Ų buried · 48 hydrogen bonds · protein-protein
- B–S · 3066 Ų buried · 44 hydrogen bonds · protein-protein
- A–T · 3066 Ų buried · 47 hydrogen bonds · protein-protein
- F–T · 718 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5IJ8 · Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone… · the same entry in another collection · chain T against T, TM-score 1.00
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q15022 · AlphaFold monomer V2.0 prediction for polycomb protein SUZ12 (Q15022) · a predicted model of the same protein · chain S against A, TM-score 0.95
- 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 0.95
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 G1KPH4
- Every structure of UniProt Q15910
- Every structure of UniProt O75530
- Every structure of UniProt Q15022
- Elsewhere: RCSB PDB 5IJ8 · PDBe 5IJ8 · UniProt G1KPH4 · UniProt Q15910 · UniProt O75530 · UniProt Q15022
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