MolNFT v1 · #164935 · protein
Crystal structure of DOT1L in complex with an inhibitor (compound 3).
6TE6 · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with an inhibitor (compound 3).”. X-ray diffraction, 1 ligand (N4W), 5 pockets (best druggability 0.80). MolNFT v1 #164935 on…
- PDB
- 6TE6
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- 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
- N4W
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | 319 | 47% helix, 16% strand | Q8TEK3 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 323 | 46% helix, 15% strand | Q8TEK3 |
Ligands and binding sites
- N4W · ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 721 | 0.80 | 0.84 | 77 | N4W |
| 2 | 1114 | 0.79 | 0.81 | 97 | empty |
| 3 | 619 | 0.79 | 0.84 | 71 | N4W |
| 4 | 96 | 0.55 | 0.85 | 17 | empty |
| 5 | 67 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1597 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6TE6 · Crystal structure of Dot1L in complex with an inhibitor (compound 3). · 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 0.94
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 6TE6 · PDBe 6TE6 · UniProt Q8TEK3
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