MolNFT v1 · #71774 · protein
Human G9A-like (glp, also known as EHMT1) in complex with inhibitor E72
3MO5 · Histone-lysine N-methyltransferase, H3 lysine-9 specific 5: “Human G9A-like (glp, also known as EHMT1) in complex with inhibitor E72”. X-ray diffraction, 3 ligands (E72, SAH, ZN), 14 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 3MO5
- Type
- protein
- Length
- 1,027 residues
- Chains
- 4
- 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
- E72, SAH, ZN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 26% 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 | 255 | 10% helix, 25% strand | Q9H9B1 |
| B | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 258 | 10% helix, 26% strand | Q9H9B1 |
| C | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 258 | 10% helix, 26% strand | Q9H9B1 |
| D | Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 (EC 2.1.1.43) | protein | 256 | 10% helix, 26% strand | Q9H9B1 |
Ligands and binding sites
- E72 · 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains C, 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.81 | 0.83 | 95 | empty |
| 2 | 1182 | 0.79 | 0.80 | 98 | empty |
| 3 | 543 | 0.70 | 0.80 | 76 | empty |
| 4 | 552 | 0.67 | 0.77 | 60 | E72 |
| 5 | 489 | 0.66 | 0.78 | 54 | SAH, E72 |
Interfaces
5 interfaces between chains.
- C–D · 1093 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1085 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 377 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3MO5 · Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 · 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 D 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 3MO5 · PDBe 3MO5 · UniProt Q9H9B1
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