Research workbench
Structure of camp-dependent protein kinase, alpha-catalytic subunit in complex with H89 protein kinase inhibitor N-[2- (4-BROMOCINNAMYLAMINO)ETHYL]-5-isoquinoline
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
- 1YDT
- 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, P04541
- Ligands
- IQB
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | C-AMP-dependent protein kinase (EC 2.7.1.37) | protein | 336 | 39% helix, 16% strand | P00517 |
| I | Protein kinase inhibitor peptide | protein | 20 | 30% helix, 0% strand | P04541 |
Ligands and binding sites
- IQB · N-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline sulfonamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.81 | 0.89 | 41 | IQB |
| 2 | 123 | 0.51 | 0.81 | 23 | empty |
| 3 | 61 | 0.41 | 0.80 | 12 | empty |
| 4 | 68 | 0.32 | 0.75 | 18 | empty |
| 5 | 66 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- E–I · 1007 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1YDT · Structure of camp-dependent protein kinase, alpha-catalytic subunit in complex with H89… · the same entry in another collection · chain E against E, 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 P00517
- Every structure of UniProt P04541
- Elsewhere: RCSB PDB 1YDT · PDBe 1YDT · UniProt P00517 · UniProt P04541
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.