Research workbench
RIP2 kinase catalytic domain (1 - 310) complex with biphenylsulfonamide
Analyse RIP2 kinase catalytic domain (1 - 310) complex with biphenylsulfonamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AR8
- Type
- protein
- Length
- 529 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, 2.7.11.1
- UniProt
- O43353
- Ligands
- XYW
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 255 | 38% helix, 16% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 274 | 41% helix, 16% strand | O43353 |
Ligands and binding sites
- XYW · 2,6-bis(fluoranyl)-N-[3-[5-[2-[(3-methylsulfonylphenyl)amino]pyrimidin-4-yl]-2-morpholin-4-yl-1,3-thiazol-4-yl]phenyl]benzenesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.81 | 0.82 | 77 | empty |
| 2 | 445 | 0.72 | 0.82 | 47 | XYW |
| 3 | 378 | 0.68 | 0.81 | 42 | XYW |
| 4 | 90 | 0.41 | 0.78 | 16 | empty |
| 5 | 103 | 0.40 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1653 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5AR8 · RIP2 Kinase Catalytic Domain (1 - 310) complex with Biphenylsulfonamide · 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 0.99
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 5AR8 · PDBe 5AR8 · UniProt O43353
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