MolNFT v1 · #137997 · protein
Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases
5W5J · Receptor-interacting SERINE/THREONINE-protein kinase 2: “Identification of potent and selective RIPK2 inhibitors for the treatment of inflammatory diseases”. X-ray diffraction, 2 ligands (9WS, SO4), 5 pockets (best druggability…
- 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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