MolNFT v1 · #63957 · protein
G9A-like protein lysine methyltransferase inhibition by bix- 01294
3FPD · Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: “G9A-like protein lysine methyltransferase inhibition by bix- 01294”. X-ray diffraction, 3 ligands (SAH, Q4A, ZN), 9 pockets (best druggability 0.81). MolNFT v1 #63957 on…
- PDB
- 3FPD
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
- EC
- 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- SAH, Q4A, ZN
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 261 | 9% helix, 26% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 260 | 10% helix, 26% strand | Q9H9B1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- Q4A · N-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.81 | 0.82 | 94 | empty |
| 2 | 201 | 0.55 | 0.78 | 25 | SAH |
| 3 | 218 | 0.54 | 0.77 | 38 | Q4A |
| 4 | 187 | 0.53 | 0.78 | 34 | Q4A |
| 5 | 173 | 0.50 | 0.77 | 23 | SAH |
Interfaces
1 interface between chains.
- A–B · 1096 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3FPD · G9a-like protein lysine methyltransferase inhibition by BIX-01294 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H9B1 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase EHMT1 (Q9H9B1) · 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 Q9H9B1
- Elsewhere: RCSB PDB 3FPD · PDBe 3FPD · UniProt Q9H9B1
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