MolNFT v1 · #124345 · protein
SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density
5KCH · Histone-lysine N-methyltransferase SETDB1: “SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into…”. X-ray diffraction, 3 ligands (6RN, UNX, SO4), 3 pockets (best druggability…
- PDB
- 5KCH
- 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
- 6RN, UNX, SO4
- Pockets
- 3 · best druggability 0.57
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
- 6RN · 4-methoxy-N-[(pyridin-2-yl)methyl]aniline · ligand · chains A
- UNX · Unknown atom or ion · ion · 50 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 157 | 0.57 | 0.82 | 20 | UNX, 6RN |
| 2 | 51 | 0.36 | 0.79 | 13 | UNX |
| 3 | 68 | 0.29 | 0.73 | 14 | UNX |
Compared structures
- 5KCH · 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 5KCH · PDBe 5KCH · UniProt Q15047
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.