Research workbench
A positive allosteric modulator binding pocket in SK2 ion channels is shared by riluzole and cyppa
Analyse A positive allosteric modulator binding pocket in SK2 ion channels is shared by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V03
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small conductance calcium-activated potassium channel protein 2; Calmodulin
- UniProt
- Q9H2S1, P62158
- Ligands
- 658, CA, SO4
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Small conductance calcium-activated potassium channel protein 2 | protein | 86 | 80% helix, 2% strand | Q9H2S1 |
| R | Calmodulin | protein | 145 | 57% helix, 7% strand | P62158 |
Ligands and binding sites
- 658 · N-(4-chlorophenyl)-2-(3,5-dimethyl-1H-pyrazol-1-yl) pyrimidin-4-amine · ligand · chains B, R
- CA · Calcium ion · metal · 2 copies · chains R
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.62 | 0.83 | 27 | 658 |
Interfaces
1 interface between chains.
- B–R · 1269 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5V03 · A positive allosteric modulator binding pocket in SK2 ion channels is shared by Riluzole… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9H2S1 · AlphaFold monomer V2.0 prediction for small conductance calcium- activated potassium… · a predicted model of the same protein · chain B against A, TM-score 0.71
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 Q9H2S1
- Every structure of UniProt P62158
- Elsewhere: RCSB PDB 5V03 · PDBe 5V03 · UniProt Q9H2S1 · UniProt P62158
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