MolNFT v1 · #188018 · protein
Structure of human glp set-domain (EHMT1) in complex with covalent inhibitor (compound 1)
7T7M · Histone-lysine N-methyltransferase EHMT1: “Structure of human glp set-domain (EHMT1) in complex with covalent inhibitor (compound 1)”. X-ray diffraction, 3 ligands (G4R, G5U, ZN), 16 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 7T7M
- Type
- protein
- Length
- 1,041 residues
- Chains
- 4
- 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
- G4R, G5U, ZN
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 260 | 10% helix, 27% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 259 | 10% helix, 25% strand | Q9H9B1 |
| C | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 260 | 10% helix, 25% strand | Q9H9B1 |
| D | Histone-lysine N-methyltransferase EHMT1 (EC 2.1.1.-, 2.1.1.43) | protein | 262 | 10% helix, 26% strand | Q9H9B1 |
Ligands and binding sites
- G4R · N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide · ligand · 3 copies · chains A, B, C
- G5U · N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl) propanamide · ligand · chains D
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.78 | 0.83 | 101 | empty |
| 2 | 369 | 0.73 | 0.85 | 49 | empty |
| 3 | 430 | 0.69 | 0.80 | 41 | G4R |
| 4 | 532 | 0.68 | 0.78 | 60 | G5U |
| 5 | 493 | 0.67 | 0.78 | 58 | G4R |
Interfaces
4 interfaces between chains.
- A–D · 1064 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 541 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 266 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7T7M · Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1) · the same entry in another collection · chain D against D, 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 B 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 Q9H9B1
- Elsewhere: RCSB PDB 7T7M · PDBe 7T7M · UniProt Q9H9B1
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