MolNFT v1 · #116898 · protein
Crystal structure of DOT1L in complex with inhibitor CPD3 [N-(1-(2- chlorophenyl)-1H-indol-6-yl)-2-(2-(5-(2-chlorophenyl)-1H-tetrazol-1- YL)ACETYL)HYDRAZINECARBOXAMIDE]
5DRY · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Crystal structure of DOT1L in complex with inhibitor CPD3 [N-(1-(2…”. X-ray diffraction, 2 ligands (5EK, K), 3 pockets (best druggability 0.84). MolNFT v1 #116898 on…
- PDB
- 5DRY
- Type
- protein
- Length
- 640 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
- 5EK, K
- Pockets
- 3 · best druggability 0.84
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 | 319 | 45% helix, 15% strand | Q8TEK3 |
| B | Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) | protein | 321 | 44% helix, 15% strand | Q8TEK3 |
Ligands and binding sites
- 5EK · N-[1-(2-chlorophenyl)-1H-indol-6-yl]-2-{[5-(2-chlorophenyl)-1H-tetrazol-1-yl]acetyl}hydrazinecarboxamide · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.84 | 0.84 | 115 | 5EK |
| 2 | 856 | 0.80 | 0.82 | 79 | 5EK |
| 3 | 88 | 0.32 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1644 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DRY · Crystal structure of Dot1L in complex with inhibitor CPD3… · 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 5DRY · PDBe 5DRY · UniProt Q8TEK3
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