Research workbench
Crystal structure of DOT1L in complex with EPZ000004
Analyse Crystal structure of DOT1L in complex with EPZ000004 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EK9
- Type
- protein
- Length
- 325 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
- EP4, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 325 | 43% helix, 15% strand | Q8TEK3 |
Ligands and binding sites
- EP4 · 5'-deoxy-5'-(dimethylamino)adenosine · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains 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 | 324 | 0.66 | 0.81 | 56 | EP4 |
| 2 | 115 | 0.46 | 0.79 | 12 | SO4 |
| 3 | 159 | 0.45 | 0.75 | 16 | empty |
| 4 | 52 | 0.31 | 0.77 | 12 | empty |
| 5 | 50 | 0.28 | 0.75 | 16 | empty |
Compared structures
- 4EK9 · Crystal structure of DOT1L in complex with EPZ000004 · 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 4EK9 · PDBe 4EK9 · UniProt Q8TEK3
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