Research workbench
Structure of human G9A set-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1- methylpiperidin-4-YL)QUINAZOLINE-2,4-diamine
Analyse Structure of human G9A set-domain (EHMT2) in complex with inhibitor 17… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VSE
- Type
- protein
- Length
- 540 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.-, 2.1.1.43
- UniProt
- Q96KQ7
- Ligands
- SAM, 9HG, ZN
- Pockets
- 8 · 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.-, 2.1.1.43) | protein | 269 | 13% helix, 25% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-, 2.1.1.43) | protein | 271 | 14% helix, 25% strand | Q96KQ7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 9HG · N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine · 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.80 | 0.82 | 72 | empty |
| 2 | 447 | 0.65 | 0.78 | 57 | SAM, 9HG |
| 3 | 399 | 0.63 | 0.78 | 52 | SAM, 9HG |
| 4 | 77 | 0.42 | 0.80 | 20 | empty |
| 5 | 114 | 0.41 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1204 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5VSE · Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17… · 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 B against A, TM-score 1.00
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 5VSE · PDBe 5VSE · UniProt Q96KQ7
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