Research workbench
Crystal structure of SETDB1 tudor domain in complexed with compound 1.
Analyse Crystal structure of SETDB1 tudor domain in complexed with compound 1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C9N
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETDB1
- EC
- 2.1.1.-
- UniProt
- Q15047
- Ligands
- FN9
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.-) | protein | 215 | 14% helix, 46% strand | Q15047 |
Ligands and binding sites
- FN9 · 3,5-dimethyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]pyrrolo[3,2-d]pyrimidin-4-one · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.85 | 0.86 | 88 | FN9 |
| 2 | 68 | 0.36 | 0.77 | 14 | empty |
| 3 | 54 | 0.35 | 0.78 | 12 | empty |
| 4 | 67 | 0.31 | 0.74 | 16 | empty |
| 5 | 52 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 888 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7C9N · Crystal structure of SETDB1 tudor domain in complexed with Compound 1. · the same entry in another collection · chain B against B, TM-score 1.00
- Q15047 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETDB1 (Q15047) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q15047
- Elsewhere: RCSB PDB 7C9N · PDBe 7C9N · UniProt Q15047
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