Research workbench
Crystal structure of AP2 associated kinase 1 isoform 1 complexed with ligand N-[3-methoxy-4-(1,3-oxazol-5-YL)PHENYL]-3-(propan-2-YL)PIPERIDINE-2-carboxamide
Analyse Crystal structure of AP2 associated kinase 1 isoform 1 complexed with ligand… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LVH
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Mus musculus
- Molecule
- AP2-associated protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q3UHJ0
- Ligands
- YFS, YFV, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.65 · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AP2-associated protein kinase 1 (EC 2.7.11.1) | protein | 284 | 37% helix, 19% strand | Q3UHJ0 |
| B | AP2-associated protein kinase 1 (EC 2.7.11.1) | protein | 281 | 38% helix, 20% strand | Q3UHJ0 |
Ligands and binding sites
- YFS · N-[3-methoxy-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide · ligand · chains A
- YFV · 5-[(4-aminopiperidin-1-yl)methyl]-N-{3-[5-(propan-2-yl)-1,3,4-thiadiazol-2-yl]phenyl}pyrrolo[2,1-F][1,2, 4]triazin-4-amine · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.68 | 0.77 | 54 | empty |
| 2 | 346 | 0.64 | 0.79 | 39 | YFS |
| 3 | 378 | 0.63 | 0.78 | 38 | YFV |
| 4 | 59 | 0.40 | 0.81 | 16 | empty |
| 5 | 50 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 287 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LVH · Crystal structure of AP2 associated kinase 1 isoform 1 complexed with ligand… · the same entry in another collection · chain A against A, TM-score 1.00
- Q3UHJ0 · AlphaFold monomer V2.0 prediction for AP2-associated protein kinase 1 (Q3UHJ0) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q3UHJ0
- Elsewhere: RCSB PDB 7LVH · PDBe 7LVH · UniProt Q3UHJ0
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