MolNFT v1 · #68755 · protein
Discovery of a 2,4-diamino-7-aminoalkoxy-quinazoline as a potent inhibitor of histone lysine methyltransferase, G9A
3K5K · Histone-lysine N-methyltransferase, H3 lysine-9 specific 3: “Discovery of a 2,4-diamino-7-aminoalkoxy-quinazoline as a potent inhibitor of histone lysine…”. X-ray diffraction, 5 ligands (SAH, DXQ, ZN), 10 pockets (best druggability…
- PDB
- 3K5K
- Type
- protein
- Length
- 541 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
- EC
- 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAH, DXQ, ZN, CL, UNX
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43) | protein | 272 | 13% helix, 25% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (EC 2.1.1.43) | protein | 269 | 13% helix, 25% strand | Q96KQ7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- DXQ · 7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.81 | 0.82 | 76 | empty |
| 2 | 252 | 0.56 | 0.78 | 39 | DXQ |
| 3 | 176 | 0.53 | 0.79 | 22 | SAH |
| 4 | 178 | 0.52 | 0.78 | 21 | SAH |
| 5 | 195 | 0.52 | 0.77 | 37 | DXQ |
Interfaces
1 interface between chains.
- A–B · 1184 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3K5K · Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96KQ7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT2 (Q96KQ7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q96KQ7
- Elsewhere: RCSB PDB 3K5K · PDBe 3K5K · UniProt Q96KQ7
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