Research workbench
Crystal structure of SET7/9 in complex with a cyproheptadine derivative
Analyse Crystal structure of SET7/9 in complex with a cyproheptadine derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YLT
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- 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
- SFG, C7N
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD7 (EC 2.1.1.43) | protein | 247 | 12% helix, 39% strand | Q8WTS6 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains A
- C7N · 2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3, 8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.63 | 0.78 | 44 | SFG, C7N, GOL |
| 2 | 66 | 0.32 | 0.75 | 14 | empty |
Compared structures
- 5YLT · Crystal structure of SET7/9 in complex with a cyproheptadine derivative · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.96
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 5YLT · PDBe 5YLT · UniProt Q8WTS6
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