Research workbench
SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1- (pyrrolidin-1-YL)PROPAN-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine
Analyse SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E47
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD7
- EC
- 2.1.1.43
- UniProt
- Q8WTS6
- Ligands
- SAM, 0N6, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 246 | 12% helix, 38% strand | Q8WTS6 |
| B | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 245 | 13% helix, 38% strand | Q8WTS6 |
| C | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 245 | 12% helix, 38% strand | Q8WTS6 |
| D | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 250 | 12% helix, 38% strand | Q8WTS6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
- 0N6 · (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.77 | 0.83 | 78 | BME, SAM |
| 2 | 610 | 0.76 | 0.83 | 67 | SAM |
| 3 | 280 | 0.66 | 0.82 | 33 | empty |
| 4 | 238 | 0.59 | 0.80 | 31 | empty |
| 5 | 82 | 0.51 | 0.83 | 18 | 0N6 |
Interfaces
4 interfaces between chains.
- A–B · 780 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 575 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 342 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 271 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4E47 · SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8WTS6 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD7 (Q8WTS6) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q8WTS6
- Elsewhere: RCSB PDB 4E47 · PDBe 4E47 · UniProt Q8WTS6
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