MolNFT v1 · #109200 · protein
Structure-guided DOT1L probe optimization by label-free ligand displacement
4WVL · Histone-lysine N-methyltransferase, H3 lysine-79 specific: “Structure-guided DOT1L probe optimization by label-free ligand displacement”. X-ray diffraction, 2 ligands (3US, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #109200…
- PDB
- 4WVL
- Type
- protein
- Length
- 331 residues
- Chains
- 1
- 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
- 3US, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 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 | 331 | 45% helix, 15% strand | Q8TEK3 |
Ligands and binding sites
- 3US · N-[4-(acetylamino)butyl]-5'-[(3-{[(4-tert-butylphenyl) carbamoyl]amino}propyl)(propan-2-yl)amino]-5'-deoxyadenosine · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.69 | 0.78 | 48 | 3US |
| 2 | 59 | 0.31 | 0.76 | 13 | empty |
| 3 | 62 | 0.28 | 0.73 | 12 | empty |
Compared structures
- 4WVL · Structure-Guided DOT1L Probe Optimization by Label-Free Ligand Displacement · 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 0.97
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 4WVL · PDBe 4WVL · UniProt Q8TEK3
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