MolNFT v1 · #156672 · protein
Glp methyltransferase with inhibitor EML741-P212121 crystal form
6MBO · Histone-lysine N-methyltransferase EHMT1: “Glp methyltransferase with inhibitor EML741-P212121 crystal form”. X-ray diffraction, 3 ligands (JDG, SAH, ZN), 7 pockets (best druggability 0.80). MolNFT v1 #156672 on GenesisL1: 3D…
- PDB
- 6MBO
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase EHMT1
- EC
- 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- JDG, SAH, 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 2.1.1.43) | protein | 261 | 10% helix, 26% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.43) | protein | 258 | 10% helix, 27% strand | Q9H9B1 |
Ligands and binding sites
- JDG · 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine · ligand · 4 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 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 | 972 | 0.80 | 0.82 | 103 | EDO |
| 2 | 502 | 0.68 | 0.78 | 56 | JDG, SAH, EDO |
| 3 | 508 | 0.66 | 0.77 | 59 | JDG, SAH, EDO |
| 4 | 100 | 0.41 | 0.77 | 22 | EDO |
| 5 | 82 | 0.38 | 0.77 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1037 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6MBO · GLP Methyltransferase with Inhibitor EML741-P212121 Crystal Form · 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 6MBO · PDBe 6MBO · UniProt Q9H9B1
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