Research workbench
Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases
Analyse Identification of potent and selective RIPK2 inhibitors for the treatment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W5J
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 2
- EC
- 2.7.10.2
- UniProt
- O43353
- Ligands
- 9WS, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2) | protein | 251 | 38% helix, 15% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2) | protein | 257 | 41% helix, 16% strand | O43353 |
Ligands and binding sites
- 9WS · N-(2-chlorophenyl)pyrazolo[1,5-a]pyridine-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.80 | 0.81 | 92 | empty |
| 2 | 470 | 0.72 | 0.81 | 45 | 9WS |
| 3 | 235 | 0.65 | 0.83 | 28 | 9WS |
| 4 | 95 | 0.42 | 0.78 | 17 | empty |
| 5 | 84 | 0.41 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1597 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5W5J · Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory… · the same entry in another collection · chain A against A, TM-score 1.00
- O43353 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O43353
- Elsewhere: RCSB PDB 5W5J · PDBe 5W5J · UniProt O43353
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