Research workbench
Crystal structure of human DOT1L in complex with a selective inhibitor
Analyse Crystal structure of human DOT1L in complex with a selective inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SR4
- Type
- protein
- Length
- 328 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-79 specific
- EC
- 2.1.1.43
- UniProt
- Q8TEK3
- Ligands
- TT8, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 328 | 42% helix, 16% strand | Q8TEK3 |
Ligands and binding sites
- TT8 · (2S)-2-azanyl-4-[[(2S,3S,4R,5R)-5-[6-(methylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.67 | 0.81 | 55 | TT8 |
| 2 | 108 | 0.46 | 0.79 | 15 | empty |
| 3 | 96 | 0.37 | 0.74 | 11 | empty |
| 4 | 54 | 0.30 | 0.76 | 13 | GOL |
Compared structures
- 3SR4 · Crystal Structure of Human DOT1L in Complex with a Selective Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TEK3 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase, H3 lysine-79… · 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 Q8TEK3
- Elsewhere: RCSB PDB 3SR4 · PDBe 3SR4 · UniProt Q8TEK3
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