Research workbench
Protein kinase a bound to (R)-1-(1H-indol-3-ylmethyl)-2-(2- pyridin-4-yl-[1,7]NAPHTYRIDIN-5-yloxy)-ehylamine
Analyse Protein kinase a bound to (R)-1-(1H-indol-3-ylmethyl)-2-(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F7Z
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase, alpha-catalytic subunit; Pki, inhibitory peptide
- EC
- 2.7.1.37
- UniProt
- P00517
- Ligands
- 6EA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Camp-dependent protein kinase, alpha-catalytic subunit (EC 2.7.1.37) | protein | 336 | 37% helix, 16% strand | P00517 |
| I | Pki, inhibitory peptide | protein | 20 | 35% helix, 5% strand | — |
Ligands and binding sites
- 6EA · (1S)-1-(1H-indol-3-ylmethyl)-2-(2-pyridin-4-yl-[1,7]naphtyridin-5-yloxy)-ehylamine · ligand · chains E
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 | 415 | 0.80 | 0.89 | 41 | 6EA |
| 2 | 104 | 0.45 | 0.79 | 19 | empty |
| 3 | 57 | 0.39 | 0.79 | 12 | empty |
| 4 | 55 | 0.33 | 0.77 | 12 | empty |
| 5 | 61 | 0.31 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- E–I · 984 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2F7Z · Protein Kinase A bound to (R)-1-(1H-Indol-3-ylmethyl)-2-(2-pyridin-4-yl-[1,7]naphtyridin-5… · the same entry in another collection · chain E against E, 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 2F7Z · PDBe 2F7Z · UniProt P00517
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