Research workbench
RIP2 kinase catalytic domain (1 - 310) complex with biaryl urea
Analyse RIP2 kinase catalytic domain (1 - 310) complex with biaryl urea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AR7
- Type
- protein
- Length
- 556 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
- SR8
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% 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 | 278 | 40% helix, 17% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 278 | 40% helix, 18% strand | O43353 |
Ligands and binding sites
- SR8 · 1-(5-tert-butyl-1,2-oxazol-3-yl)-3-(4-pyridin-4-yloxyphenyl)urea · ligand · 2 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 | 1025 | 0.83 | 0.84 | 89 | empty |
| 2 | 269 | 0.72 | 0.86 | 39 | SR8 |
| 3 | 354 | 0.69 | 0.82 | 47 | SR8 |
| 4 | 109 | 0.39 | 0.75 | 21 | empty |
| 5 | 51 | 0.29 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1915 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5AR7 · RIP2 Kinase Catalytic Domain (1 - 310) complex with Biaryl Urea · 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 0.98
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 5AR7 · PDBe 5AR7 · UniProt O43353
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