MolNFT v1 · #25055 · protein
Crystal structure of protein kinase a in complex with azepane derivative 5
1VEB · Camp-dependent protein kinase, alpha-catalytic subunit: “Crystal structure of protein kinase a in complex with azepane derivative 5”. X-ray diffraction, 1 ligand (I05), 4 pockets (best druggability 0.80). MolNFT v1 #25055 on…
- PDB
- 1VEB
- Type
- protein
- Length
- 361 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, P04541
- Ligands
- I05
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 341 | 38% helix, 16% strand | P00517 |
| B | Camp-dependent protein kinase inhibitor, alpha form | protein | 20 | 35% helix, 5% strand | P04541 |
Ligands and binding sites
- I05 · (3R,4R)-N-{4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzyloxy]-azepan-3-yl}-isonicotinamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.80 | 0.89 | 41 | I05 |
| 2 | 127 | 0.52 | 0.80 | 18 | empty |
| 3 | 66 | 0.38 | 0.79 | 12 | empty |
| 4 | 62 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1051 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 1VEB · Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 5 · the same entry in another collection · chain A against A, 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 1VEB · PDBe 1VEB · UniProt P00517 · UniProt P04541
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