Research workbench
Crystal structures of protein kinase B selective inhibitors in complex with protein kinase a and mutants
Analyse Crystal structures of protein kinase B selective inhibitors in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XH5
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Camp-dependent protein kinase…
- EC
- 2.7.1.37
- UniProt
- P00517, P61925
- Ligands
- R68
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) | protein | 337 | 36% helix, 16% strand | P00517 |
| B | Camp-dependent protein kinase inhibitor, alpha form | protein | 20 | 35% helix, 0% strand | P61925 |
Ligands and binding sites
- R68 · N-{4-[(4-{3-[(2R)-3,3-dimethylpiperidin-2-yl]-2-fluoro-6-hydroxybenzoyl}benzoyl)amino]azepan-3-yl}isonicotinamide · ligand · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.79 | 0.87 | 46 | R68 |
| 2 | 82 | 0.46 | 0.80 | 12 | empty |
| 3 | 89 | 0.41 | 0.79 | 19 | BU3 |
| 4 | 61 | 0.31 | 0.76 | 22 | empty |
| 5 | 65 | 0.30 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 934 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1XH5 · Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P61925 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain B against A, TM-score 0.40
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 P00517
- Every structure of UniProt P61925
- Elsewhere: RCSB PDB 1XH5 · PDBe 1XH5 · UniProt P00517 · UniProt P61925
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