Research workbench
Crystal structure of human KDM4A in complex with compound 16
Analyse Crystal structure of human KDM4A in complex with compound 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2W
- Type
- protein
- Length
- 1,391 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
- 5UP, ZN
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 341 | 31% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 31% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 30% helix, 24% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 31% helix, 24% strand | O75164 |
Ligands and binding sites
- 5UP · 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 29 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.72 | 0.82 | 43 | ZN, 5UP, EDO |
| 2 | 374 | 0.72 | 0.83 | 40 | ZN, 5UP, EDO |
| 3 | 476 | 0.72 | 0.81 | 44 | ZN, 5UP, EDO |
| 4 | 303 | 0.69 | 0.83 | 34 | ZN, 5UP, EDO |
| 5 | 407 | 0.66 | 0.79 | 50 | EDO |
Interfaces
3 interfaces between chains.
- B–D · 504 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 271 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 200 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5F2W · Crystal structure of human KDM4A in complex with compound 16 · 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 5F2W · PDBe 5F2W · UniProt O75164
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