Research workbench
Crystal structure of JMJD2A complexed with inhibitor
Analyse Crystal structure of JMJD2A complexed with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RVH
- Type
- protein
- Length
- 701 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- HQ2, NI, ZN
- Pockets
- 9 · best druggability 0.72
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.-) | protein | 351 | 29% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- HQ2 · 8-hydroxy-3-(piperazin-1-yl)quinoline-5-carboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.72 | 0.77 | 79 | GOL |
| 2 | 374 | 0.72 | 0.83 | 41 | NI, HQ2 |
| 3 | 411 | 0.70 | 0.82 | 39 | NI, HQ2 |
| 4 | 105 | 0.50 | 0.81 | 22 | empty |
| 5 | 53 | 0.45 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RVH · Crystal Structure of JMJD2A Complexed with Inhibitor · 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 3RVH · PDBe 3RVH · UniProt O75164
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