Research workbench
Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP18
Analyse Structure of the kinase domain of human RIPK2 in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FU5
- Type
- protein
- Length
- 568 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
- E7N
- Pockets
- 8 · 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 2.7.11.1, 2.7.10.2) | protein | 282 | 41% helix, 17% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 2.7.10.2) | protein | 286 | 40% helix, 16% strand | O43353 |
Ligands and binding sites
- E7N · ~{N}-[5-[2-azanyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]-2-methoxy-phenyl]propane-1-sulfonamide · 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 | 1095 | 0.83 | 0.84 | 80 | empty |
| 2 | 276 | 0.69 | 0.84 | 31 | E7N |
| 3 | 302 | 0.68 | 0.83 | 29 | E7N |
| 4 | 132 | 0.48 | 0.78 | 29 | empty |
| 5 | 101 | 0.38 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2042 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6FU5 · Structure of the kinase domain of human RIPK2 in complex with the inhibitor CSLP18 · the same entry in another collection · chain A against A, TM-score 1.00
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 6FU5 · PDBe 6FU5 · UniProt O43353
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