MolNFT v1 · #151240 · protein
Crystal structure of RIP1 kinase in complex with GSK547
6HHO · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Crystal structure of RIP1 kinase in complex with GSK547”. X-ray diffraction, 1 ligand (G4W), 6 pockets (best druggability 0.76). MolNFT v1 #151240 on GenesisL1: 3D structure…
- PDB
- 6HHO
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 1
- EC
- 2.7.11.1
- UniProt
- Q13546
- Ligands
- G4W
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 273 | 42% helix, 18% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 266 | 42% helix, 16% strand | Q13546 |
Ligands and binding sites
- G4W · 6-[4-[(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]carbonylpiperidin-1-yl]pyrimidine-4-carbonitrile · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.76 | 0.78 | 85 | empty |
| 2 | 225 | 0.74 | 0.89 | 29 | G4W |
| 3 | 377 | 0.72 | 0.83 | 44 | G4W |
| 4 | 119 | 0.40 | 0.75 | 23 | empty |
| 5 | 58 | 0.36 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 333 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6HHO · Crystal structure of RIP1 kinase in complex with GSK547 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13546 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q13546
- Elsewhere: RCSB PDB 6HHO · PDBe 6HHO · UniProt Q13546
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