Research workbench
Crystal structure of human KDM4A in complex with compound 19A
Analyse Crystal structure of human KDM4A in complex with compound 19A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H4T
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- FOW, ZN, CL
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 340 | 31% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 338 | 33% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 342 | 30% helix, 25% strand | O75164 |
Ligands and binding sites
- FOW · 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)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 · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.74 | 0.79 | 73 | ZN, FOW |
| 2 | 465 | 0.74 | 0.83 | 42 | ZN, FOW |
| 3 | 414 | 0.72 | 0.83 | 40 | ZN, FOW |
| 4 | 403 | 0.71 | 0.82 | 39 | ZN, FOW |
| 5 | 434 | 0.60 | 0.75 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–C · 527 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 283 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 185 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6H4T · Crystal structure of human KDM4A in complex with compound 19a · 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 6H4T · PDBe 6H4T · UniProt O75164
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