Research workbench
Crystal structure of EHMT2 set domain in complex with compound 10
Analyse Crystal structure of EHMT2 set domain in complex with compound 10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DCF
- Type
- protein
- Length
- 519 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.-
- UniProt
- Q96KQ7
- Ligands
- SAM, H30, ZN
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-) | protein | 260 | 10% helix, 24% strand | Q96KQ7 |
| B | Histone-lysine N-methyltransferase EHMT2 (EC 2.1.1.-) | protein | 259 | 11% helix, 27% strand | Q96KQ7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- H30 · 5'-methoxy-6'-(1-methyl-2,3,4,7-tetrahydroazepin-5-yl) spiro[cyclobutane-1,3'-indole]-2'-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 | 963 | 0.80 | 0.82 | 71 | empty |
| 2 | 453 | 0.67 | 0.79 | 50 | SAM, H30 |
| 3 | 251 | 0.60 | 0.79 | 34 | H30 |
| 4 | 182 | 0.53 | 0.78 | 21 | SAM |
| 5 | 158 | 0.46 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1249 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7DCF · Crystal structure of EHMT2 SET domain in complex with compound 10 · the same entry in another collection · chain B against B, 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 7DCF · PDBe 7DCF · UniProt Q96KQ7
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