Research workbench
Crystal structure of histone lysine methyltransferase G9A with an inhibitor
Analyse Crystal structure of histone lysine methyltransferase G9A with an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJW
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT2
- EC
- 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAH, CIQ, ZN, UNX
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.43) | protein | 268 | 12% helix, 26% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.43) | protein | 270 | 15% helix, 24% strand | Q96KQ7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- CIQ · 2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- UNX · Unknown atom or ion · ion · 29 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.80 | 0.82 | 82 | UNX |
| 2 | 395 | 0.62 | 0.77 | 50 | SAH, CIQ, UNX |
| 3 | 313 | 0.61 | 0.78 | 34 | SAH, CIQ |
| 4 | 96 | 0.38 | 0.76 | 13 | empty |
| 5 | 92 | 0.36 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1150 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3RJW · Crystal structure of histone lysine methyltransferase g9a with an inhibitor · 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 3RJW · PDBe 3RJW · UniProt Q96KQ7
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