MolNFT v1 · #116934 · protein
Crystal structure of DOT1L in complex with inhibitor CPD11 [N4-methyl- N2-(2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-YL)PYRIMIDINE-2,4- diamine]
5DT2 · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with inhibitor CPD11 [N4-methyl…”. X-ray diffraction, 2 ligands (5EV, SO4), 5 pockets (best druggability 0.89). MolNFT v1 #116934 on…
- PDB
- 5DT2
- Type
- protein
- Length
- 626 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
- 5EV, SO4
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% 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 | 311 | 46% helix, 14% strand | Q8TEK3 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 315 | 45% helix, 16% strand | Q8TEK3 |
Ligands and binding sites
- 5EV · N~4~-methyl-N~2~-[2-methyl-1-(2-phenoxyphenyl)-1H-indol-6-yl]pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.89 | 0.90 | 146 | 5EV |
| 2 | 53 | 0.48 | 0.86 | 16 | empty |
| 3 | 106 | 0.36 | 0.74 | 21 | empty |
| 4 | 60 | 0.29 | 0.74 | 17 | empty |
| 5 | 55 | 0.25 | 0.72 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1493 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5DT2 · Crystal structure of Dot1L in complex with inhibitor CPD11… · 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 5DT2 · PDBe 5DT2 · UniProt Q8TEK3
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