MolNFT v1 · #41112 · protein
Structure of camp-dependent protein kinase complexed with a- 443654
2JDS: “Structure of camp-dependent protein kinase complexed with a- 443654”. X-ray diffraction, 1 ligand (L20), 6 pockets (best druggability 0.80). MolNFT v1 #41112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JDS
- Type
- protein
- Length
- 357 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase; Camp-dependent protein kinase inhibitor alpha
- EC
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- L20
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase (EC 2.7.11.11) | protein | 337 | 36% helix, 16% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 10% strand | P61925 |
Ligands and binding sites
- L20 · (2S)-1-(1H-indol-3-yl)-3-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}propan-2-amine · ligand · chains A
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 | 411 | 0.80 | 0.88 | 45 | L20 |
| 2 | 63 | 0.38 | 0.78 | 13 | empty |
| 3 | 64 | 0.33 | 0.77 | 18 | empty |
| 4 | 82 | 0.31 | 0.73 | 15 | empty |
| 5 | 63 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–I · 1018 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 2JDS · Structure of cAMP-dependent protein kinase complexed with A-443654 · 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 I against A, TM-score 0.42
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 2JDS · PDBe 2JDS · UniProt P00517 · UniProt P61925
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