MolNFT v1 · #116929 · protein
Crystal structure of DOT1L in complex with inhibitor CPD10 [6'-chloro- 1,4-dimethyl-5'-(2-methyl-6-((4-(METHYLAMINO)PYRIMIDIN-2-YL)AMINO)- 1H-indol-1-yl)-[3,3'-bipyridin]-2(1H)-one]
5DSX · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with inhibitor CPD10 [6'-chloro…”. X-ray diffraction, 2 ligands (5EW, K), 5 pockets (best druggability 0.81). MolNFT v1 #116929 on…
- PDB
- 5DSX
- Type
- protein
- Length
- 637 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
- 5EW, K
- Pockets
- 5 · best druggability 0.81
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 | 316 | 45% helix, 15% strand | Q8TEK3 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 321 | 47% helix, 16% strand | Q8TEK3 |
Ligands and binding sites
- 5EW · 6'-chloro-1,4-dimethyl-5'-(2-methyl-6-{[4-(methylamino)pyrimidin-2-yl]amino}-1H-indol-1-yl)-3,3'-bipyridin-2(1H)-one · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.81 | 0.84 | 100 | empty |
| 2 | 735 | 0.78 | 0.82 | 71 | 5EW |
| 3 | 732 | 0.78 | 0.82 | 72 | 5EW |
| 4 | 82 | 0.32 | 0.74 | 17 | empty |
| 5 | 88 | 0.31 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1496 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DSX · Crystal structure of Dot1L in complex with inhibitor CPD10… · the same entry in another collection · chain B against B, 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 5DSX · PDBe 5DSX · UniProt Q8TEK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.