Research workbench
Structure of HS/ACPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1, 2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl) methyl]-3,4-dihydroisoquinolin-1(2H)-one
Analyse Structure of HS/ACPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B3W
- Type
- protein
- Length
- 1,901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enhancer of zeste 2 polycomb repressive complex 2 subunit, enhancer of zeste 2 polycomb…
- UniProt
- G1KPH4, O75530, Q15022
- Ligands
- CJG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enhancer of zeste 2 polycomb repressive complex 2 subunit, enhancer of zeste 2 polycomb repressive complex 2 subunit | protein | 463 | 32% helix, 16% strand | G1KPH4 |
| B | Enhancer of zeste 2 polycomb repressive complex 2 subunit, enhancer of zeste 2 polycomb repressive complex 2 subunit | protein | 465 | 32% helix, 16% strand | G1KPH4 |
| 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 | 59% helix, 2% strand | Q15022 |
Ligands and binding sites
- CJG · 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.86 | 0.93 | 44 | empty |
| 2 | 421 | 0.86 | 0.94 | 42 | empty |
| 3 | 400 | 0.80 | 0.89 | 60 | empty |
| 4 | 375 | 0.80 | 0.90 | 56 | empty |
| 5 | 744 | 0.77 | 0.82 | 98 | empty |
Interfaces
8 interfaces between chains.
- A–F · 3501 Ų buried · 42 hydrogen bonds · protein-protein
- B–E · 3460 Ų buried · 47 hydrogen bonds · protein-protein
- B–S · 3100 Ų buried · 46 hydrogen bonds · protein-protein
- A–T · 3058 Ų buried · 46 hydrogen bonds · protein-protein
- F–T · 675 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6B3W · Structure of Hs/AcPRC2 in complex with 5,8-dichloro-7-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(4… · 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 E 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
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 O75530
- Every structure of UniProt Q15022
- Elsewhere: RCSB PDB 6B3W · PDBe 6B3W · UniProt G1KPH4 · UniProt O75530 · UniProt Q15022
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