Research workbench
Structure of PKA with a protein kinase B-selective inhibitor.
Analyse Structure of PKA with a protein kinase B-selective inhibitor. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KKV
- Type
- protein
- Length
- 358 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Pki kinase inhibitor
- EC
- 2.7.11.11
- UniProt
- P00517
- Ligands
- B99
- Pockets
- 7 · 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 catalytic subunit alpha (EC 2.7.11.11) | protein | 338 | 37% helix, 16% strand | P00517 |
| I | Pki kinase inhibitor | protein | 20 | 30% helix, 10% strand | — |
Ligands and binding sites
- B99 · (2S)-1-{[6-furan-3-yl-5-(3-methyl-2H-indazol-5-yl)pyridin-3-yl]oxy}-3-(1H-indol-3-yl)propan-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.80 | 0.87 | 45 | B99 |
| 2 | 97 | 0.49 | 0.81 | 13 | empty |
| 3 | 104 | 0.45 | 0.79 | 25 | empty |
| 4 | 106 | 0.35 | 0.73 | 20 | empty |
| 5 | 78 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–I · 1062 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3KKV · Structure of PKA with a protein Kinase B-selective inhibitor. · 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
- Elsewhere: RCSB PDB 3KKV · PDBe 3KKV · UniProt P00517
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