MolNFT v1 · #122238 · protein
Structure of HS/ACPRC2 in complex with a pyridone inhibitor
5IJ7 · Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N…: “Structure of HS/ACPRC2 in complex with a pyridone inhibitor”. X-ray diffraction, 2 ligands (6BN, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #122238 on GenesisL1: 3D…
- PDB
- 5IJ7
- Type
- protein
- Length
- 1,904 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 0.86
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 26% 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 | 465 | 36% helix, 17% strand | G1KPH4, Q15910 |
| B | Enhancer of zeste homolog 2 (EZH2),HISTONE-lysine N- methyltransferase EZH2 (EC 2.1.1.43) | protein | 469 | 36% helix, 17% strand | G1KPH4, Q15910 |
| E | Polycomb protein eed | protein | 355 | 4% helix, 48% strand | O75530 |
| F | Polycomb protein eed | protein | 360 | 4% helix, 47% strand | O75530 |
| S | Polycomb protein SUZ12 | protein | 127 | 65% helix, 2% strand | Q15022 |
| T | Polycomb protein SUZ12 | protein | 128 | 64% 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, E, B, F
- 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.86 | 0.95 | 42 | empty |
| 2 | 404 | 0.86 | 0.95 | 43 | empty |
| 3 | 328 | 0.80 | 0.90 | 48 | empty |
| 4 | 326 | 0.79 | 0.90 | 47 | empty |
| 5 | 1066 | 0.78 | 0.80 | 123 | 6BN |
Interfaces
8 interfaces between chains.
- A–E · 3510 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 3510 Ų buried · 47 hydrogen bonds · protein-protein
- B–T · 3089 Ų buried · 47 hydrogen bonds · protein-protein
- A–S · 3072 Ų buried · 46 hydrogen bonds · protein-protein
- E–S · 713 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5IJ7 · Structure of Hs/AcPRC2 in complex with a pyridone inhibitor · the same entry in another collection · chain S against S, TM-score 1.00
- O75530 · AlphaFold monomer V2.0 prediction for polycomb protein eed (O75530) · a predicted model of the same protein · chain E against A, TM-score 1.00
- 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 5IJ7 · PDBe 5IJ7 · UniProt G1KPH4 · UniProt Q15910 · UniProt O75530 · UniProt Q15022
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