MolNFT v1 · #71769 · protein
Human G9A-like (glp, also known as EHMT1) in complex with inhibitor E11
3MO0 · Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: “Human G9A-like (glp, also known as EHMT1) in complex with inhibitor E11”. X-ray diffraction, 3 ligands (E11, SAH, ZN), 7 pockets (best druggability 0.75). MolNFT v1 #71769…
- PDB
- 3MO0
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
- EC
- 2.1.1.43
- UniProt
- Q9H9B1
- Ligands
- E11, SAH, ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 251 | 9% helix, 26% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 242 | 10% helix, 20% strand | Q9H9B1 |
Ligands and binding sites
- E11 · N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino) propyl]-6,7-dimethoxyquinazoline-2,4-diamine · ligand · 3 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 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
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 | 1153 | 0.75 | 0.78 | 84 | empty |
| 2 | 509 | 0.69 | 0.79 | 59 | SAH, E11 |
| 3 | 389 | 0.63 | 0.78 | 49 | SAH, E11 |
| 4 | 119 | 0.43 | 0.77 | 25 | empty |
| 5 | 74 | 0.43 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1040 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3MO0 · Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 · 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 0.98
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 3MO0 · PDBe 3MO0 · UniProt Q9H9B1
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