MolNFT v1 · #80777 · protein
E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 jumonji demethylase
3U78 · Lysine-specific demethylase 7: “E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 jumonji demethylase”. X-ray diffraction, 5 ligands (AKG, E67, NI), 4 pockets (best druggability 0.71). MolNFT v1 #80777 on GenesisL1…
- PDB
- 3U78
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 7
- EC
- 1.14.11.-
- UniProt
- Q6ZMT4
- Ligands
- AKG, E67, NI, CL, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 7 (EC 1.14.11.-) | protein | 366 | 41% helix, 23% strand | Q6ZMT4 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- E67 · 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.71 | 0.82 | 43 | AKG, NI, E67 |
| 2 | 83 | 0.33 | 0.74 | 20 | empty |
| 3 | 56 | 0.32 | 0.76 | 17 | empty |
| 4 | 59 | 0.25 | 0.72 | 14 | empty |
Compared structures
- 3U78 · E67-2 selectively inhibits KIAA1718, a human histone H3 lysine 9 Jumonji demethylase · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ZMT4 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 7A (Q6ZMT4) · 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 Q6ZMT4
- Elsewhere: RCSB PDB 3U78 · PDBe 3U78 · UniProt Q6ZMT4
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