Research workbench
Structure of camp-dependent protein kinase, alpha-catalytic subunit in complex with H7 protein kinase inhibitor 1-(5- isoquinolinesulfonyl)-2-methylpiperazine
Analyse Structure of camp-dependent protein kinase, alpha-catalytic subunit in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YDR
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-AMP-dependent protein kinase; Protein kinase inhibitor peptide
- EC
- 2.7.1.37
- UniProt
- P00517, P61925
- Ligands
- IQP
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | C-AMP-dependent protein kinase (EC 2.7.1.37) | protein | 336 | 37% helix, 15% strand | P00517 |
| I | Protein kinase inhibitor peptide | protein | 20 | 30% helix, 5% strand | P61925 |
Ligands and binding sites
- IQP · 1-(5-isoquinolinesulfonyl)-2-methylpiperazine · ligand · chains E
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 | 430 | 0.81 | 0.89 | 40 | IQP |
| 2 | 107 | 0.48 | 0.81 | 20 | empty |
| 3 | 62 | 0.43 | 0.81 | 11 | empty |
| 4 | 56 | 0.32 | 0.76 | 13 | empty |
| 5 | 53 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- E–I · 1029 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1YDR · Structure of camp-dependent protein kinase, alpha-catalytic subunit in complex with H7… · the same entry in another collection · chain E against E, 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 I against A, TM-score 0.37
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 1YDR · PDBe 1YDR · UniProt P00517 · UniProt P61925
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