Research workbench
Crystal structure of protein kinase a in complex with azepane derivative 1
Analyse Crystal structure of protein kinase a in complex with azepane derivative 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SVE
- Type
- protein
- Length
- 363 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
- I01, MG8, NA
- Pockets
- 5 · best druggability 0.81
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 | 344 | 38% helix, 16% strand | P00517 |
| B | Camp-dependent protein kinase inhibitor, alpha form | protein | 19 | 32% helix, 5% strand | P04541 |
Ligands and binding sites
- I01 · (4R)-4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoic acid (3R)-3-[(pyridine-4-carbonyl)amino]-azepan-4-yl ester · ligand · chains A, B
- MG8 · N-octanoyl-N-methylglucamine · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.81 | 0.90 | 40 | I01 |
| 2 | 103 | 0.55 | 0.83 | 14 | MG8 |
| 3 | 89 | 0.38 | 0.77 | 15 | empty |
| 4 | 73 | 0.30 | 0.74 | 16 | empty |
| 5 | 64 | 0.30 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 991 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 1SVE · Crystal Structure of Protein Kinase A in Complex with Azepane Derivative 1 · 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 1SVE · PDBe 1SVE · UniProt P00517 · UniProt P04541
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.