Research workbench
SRPK1 in complex with MSC2711186
Analyse SRPK1 in complex with MSC2711186 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PQS
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens
- Molecule
- SRSF protein kinase 1
- EC
- 2.7.11.1
- Ligands
- 80H, NA, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SRSF protein kinase 1 (EC 2.7.11.1) | protein | 351 | 45% helix, 17% strand | — |
Ligands and binding sites
- 80H · ~{N}-[3-[[[2-(6-chloranyl-7-fluoranyl-1~{H}-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-~{N}-methyl-methanesulfonamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- CIT · Citric acid · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.79 | 0.83 | 66 | EDO, 80H, GOL, CL |
| 2 | 707 | 0.78 | 0.83 | 68 | 80H, GOL, CL |
| 3 | 1033 | 0.73 | 0.76 | 69 | empty |
| 4 | 736 | 0.73 | 0.79 | 53 | empty |
| 5 | 662 | 0.72 | 0.79 | 56 | CIT |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7PQS · SRPK1 in complex with MSC2711186 · 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
- Elsewhere: RCSB PDB 7PQS · PDBe 7PQS
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