MolNFT v1 · #138578 · protein
Crystal structure of murine receptor-interacting protein 4 (RIPK4) D143N bound to tozasertib (vx-680)
5WNM · Receptor-interacting SERINE/THREONINE-protein kinase 4: “Crystal structure of murine receptor-interacting protein 4 (RIPK4) D143N bound to tozasertib (vx-680)”. X-ray diffraction, 2 ligands (VX6, CL), 2 pockets (best druggability…
- PDB
- 5WNM
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 4
- EC
- 2.7.11.1
- UniProt
- Q9ERK0
- Ligands
- VX6, CL
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 4 (EC 2.7.11.1) | protein | 263 | 42% helix, 16% strand | Q9ERK0 |
Ligands and binding sites
- VX6 · Cyclopropanecarboxylic acid {4-[4-(4-methyl-piperazin-1-yl)-6-(5-methyl-2H-pyrazol-3-ylamino)-pyrimidin-2-ylsulfanyl]-phenyl}-amide · ligand · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.63 | 0.80 | 30 | VX6 |
| 2 | 122 | 0.49 | 0.79 | 30 | empty |
Compared structures
- 5WNM · Crystal structure of murine receptor-interacting protein 4 (Ripk4) D143N bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ERK0 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9ERK0
- Elsewhere: RCSB PDB 5WNM · PDBe 5WNM · UniProt Q9ERK0
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