MolNFT v1 · #113717 · protein
Inhibitors of jumonjic domain-containing histone demethylases
5ANQ · Lysine-specific demethylase 4A: “Inhibitors of jumonjic domain-containing histone demethylases”. X-ray diffraction, 5 ligands (5YQ, FE2, ZN), 9 pockets (best druggability 0.74). MolNFT v1 #113717 on GenesisL1: 3D structure, binding…
- PDB
- 5ANQ
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.27
- UniProt
- O75164
- Ligands
- 5YQ, FE2, ZN, SO4, CL
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.27) | protein | 350 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.27) | protein | 344 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
- 5YQ · 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.74 | 0.83 | 44 | 5YQ, FE2 |
| 2 | 464 | 0.73 | 0.82 | 45 | 5YQ, FE2 |
| 3 | 683 | 0.71 | 0.78 | 65 | empty |
| 4 | 120 | 0.51 | 0.81 | 26 | empty |
| 5 | 53 | 0.42 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5ANQ · inhibitors of JumonjiC domain-containing histone demethylases · the same entry in another collection · 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 O75164
- Elsewhere: RCSB PDB 5ANQ · PDBe 5ANQ · UniProt O75164
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