Research workbench
Structure of PKA complexed with 4-(4-chlorobenzyl)-1-(7H- PYRROLO(2,3-D)PYRIMIDIN-4-YL)PIPERIDIN-4-ylamine
Analyse Structure of PKA complexed with 4-(4-chlorobenzyl)-1-(7H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VO7
- Type
- protein
- Length
- 357 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
- 2.7.11.11
- UniProt
- P00517, P61925
- Ligands
- M05
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.11.11) | protein | 337 | 37% helix, 16% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 35% helix, 10% strand | P61925 |
Ligands and binding sites
- M05 · 4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium · ligand · 2 copies · 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 | 343 | 0.80 | 0.89 | 39 | M05 |
| 2 | 108 | 0.44 | 0.78 | 18 | empty |
| 3 | 61 | 0.41 | 0.80 | 12 | M05 |
| 4 | 74 | 0.32 | 0.74 | 16 | empty |
| 5 | 73 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–I · 1039 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2VO7 · Structure of PKA complexed with 4-(4-Chlorobenzyl)-1-(7H-pyrrolo(2,3… · 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 0.40
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 2VO7 · PDBe 2VO7 · UniProt P00517 · UniProt P61925
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