Research workbench
Crystal structure of human KDM4A in complex with compound 16m
Analyse Crystal structure of human KDM4A in complex with compound 16m in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4S
- Type
- protein
- Length
- 1,351 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Homo sapiens
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- FQE, ZN, CL
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.45 · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 335 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 336 | 32% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 337 | 32% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 343 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
- FQE · 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.71 | 0.82 | 41 | ZN, FQE |
| 2 | 358 | 0.71 | 0.83 | 41 | ZN, FQE |
| 3 | 315 | 0.69 | 0.83 | 33 | ZN, FQE |
| 4 | 329 | 0.67 | 0.81 | 36 | ZN, FQE |
| 5 | 315 | 0.57 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 502 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 319 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 126 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6H4S · Crystal structure of human KDM4A in complex with compound 16M · 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 6H4S · PDBe 6H4S · UniProt O75164
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