MolNFT v1 · #127411 · protein
Crystal structure of DOT1L in complex with adenosine and inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-YL)QUINOLINE-4,6- diamine]
5MVS · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with adenosine and inhibitor CPD1…”. X-ray diffraction, 2 ligands (ADN, 5JJ), 4 pockets (best druggability 0.86). MolNFT v1 #127411 on…
- PDB
- 5MVS
- 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
- ADN, 5JJ
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% 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 | 320 | 45% helix, 15% strand | Q8TEK3 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 322 | 45% helix, 16% strand | Q8TEK3 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- 5JJ · N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl) quinoline-4,6-diamine · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.86 | 0.91 | 83 | 5JJ |
| 2 | 536 | 0.86 | 0.91 | 81 | 5JJ |
| 3 | 94 | 0.32 | 0.73 | 17 | empty |
| 4 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1588 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5MVS · Crystal structure of Dot1L in complex with adenosine and inhibitor CPD1… · 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 5MVS · PDBe 5MVS · UniProt Q8TEK3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.