MolNFT v1 · #135297 · protein
Structure of human glp set-domain (EHMT1) in complex with inhibitor MS0124
5TUZ · Histone-lysine N-methyltransferase EHMT1: “Structure of human glp set-domain (EHMT1) in complex with inhibitor MS0124”. X-ray diffraction, 3 ligands (SAM, 7L6, ZN), 8 pockets (best druggability 0.78). MolNFT v1 #135297 on GenesisL1…
- PDB
- 5TUZ
- Type
- protein
- Length
- 516 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, 7L6, ZN
- Pockets
- 8 · best druggability 0.78
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 | 259 | 10% helix, 27% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 257 | 10% helix, 27% strand | Q9H9B1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 7L6 · 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.78 | 0.80 | 92 | EDO |
| 2 | 396 | 0.65 | 0.79 | 50 | SAM, 7L6 |
| 3 | 289 | 0.57 | 0.77 | 41 | 7L6 |
| 4 | 241 | 0.56 | 0.78 | 26 | SAM |
| 5 | 88 | 0.44 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5TUZ · Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124 · 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 5TUZ · PDBe 5TUZ · UniProt Q9H9B1
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