MolNFT v1 · #123024 · protein
The identification and pharmacological characterization of 6-(tert- butylsulfonyl)-N-(5-fluoro-1H-indazol-3-YL)QUINOLIN-4-amine (GSK583), a highly potent and selective inhibitor of RIP2 kinase, compound 3 complex
5J79 · Receptor-interacting SERINE/THREONINE-protein kinase 2: “The identification and pharmacological characterization of 6-(tert…”. X-ray diffraction, 2 ligands (6GE, SO4), 6 pockets (best druggability 0.83). MolNFT v1 #123024 on…
- PDB
- 5J79
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 2
- EC
- 2.7.11.1, 2.7.10.2
- UniProt
- O43353
- Ligands
- 6GE, SO4
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2) | protein | 283 | 40% helix, 18% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2) | protein | 277 | 38% helix, 19% strand | O43353 |
Ligands and binding sites
- 6GE · 4-methyl-3-{[6-(methylsulfonyl)quinolin-4-yl]amino}phenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.83 | 0.84 | 77 | empty |
| 2 | 277 | 0.65 | 0.82 | 33 | 6GE |
| 3 | 332 | 0.63 | 0.79 | 37 | 6GE |
| 4 | 157 | 0.51 | 0.79 | 26 | empty |
| 5 | 106 | 0.42 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1979 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5J79 · The identification and pharmacological characterization of… · 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 B against A, TM-score 0.97
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 5J79 · PDBe 5J79 · UniProt O43353
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