Research workbench
Structure of human glp set-domain (EHMT1) in complex with inhibitor 13
Analyse Structure of human glp set-domain (EHMT1) in complex with inhibitor 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VSD
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT1
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- SAM, 9HJ, ZN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 257 | 10% helix, 26% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 258 | 10% helix, 27% strand | Q9H9B1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 9HJ · 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · chains A
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 | 951 | 0.80 | 0.82 | 89 | GOL |
| 2 | 391 | 0.65 | 0.79 | 45 | SAM, 9HJ |
| 3 | 346 | 0.63 | 0.79 | 46 | SAM, 9HJ |
| 4 | 92 | 0.42 | 0.79 | 20 | empty |
| 5 | 82 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5VSD · Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 13 · 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 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 Q9H9B1
- Elsewhere: RCSB PDB 5VSD · PDBe 5VSD · UniProt Q9H9B1
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