Research workbench
SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy
Analyse SETDB1 in complex with an early stage, low affinity fragment candidate modelled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KCO
- Type
- protein
- Length
- 212 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETDB1
- EC
- 2.1.1.43
- UniProt
- Q15047
- Ligands
- 6RO, UNX, SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETDB1 (EC 2.1.1.43) | protein | 212 | 14% helix, 47% strand | Q15047 |
Ligands and binding sites
- 6RO · ~{N}-(4-chlorophenyl)methanesulfonamide · ligand · chains A
- UNX · Unknown atom or ion · ion · 47 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.55 | 0.81 | 20 | 6RO, UNX |
| 2 | 50 | 0.36 | 0.80 | 12 | empty |
| 3 | 75 | 0.31 | 0.73 | 16 | UNX |
Compared structures
- 5KCO · SETDB1 in complex with an early stage, low affinity fragment candidate modelled at… · the same entry in another collection · chain A against A, 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 A 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 5KCO · PDBe 5KCO · UniProt Q15047
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