Research workbench
Crystal structure of human RIPK1 kinase domain in complex with a novel inhibitor
Analyse Crystal structure of human RIPK1 kinase domain in complex with a novel inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FD0
- Type
- protein
- Length
- 523 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
- 3IU
- Pockets
- 5 · best druggability 0.79
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 | 266 | 42% helix, 18% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 257 | 41% helix, 16% strand | Q13546 |
Ligands and binding sites
- 3IU · N-[(3S)-5-methyl-7-[2-(oxan-4-yl)ethynyl]-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-5-(phenylmethyl)-4H-1,2,4-triazole-3-carboxamide · 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 | 293 | 0.79 | 0.90 | 41 | 3IU |
| 2 | 786 | 0.75 | 0.80 | 76 | empty |
| 3 | 244 | 0.73 | 0.87 | 34 | 3IU |
| 4 | 67 | 0.38 | 0.79 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7FD0 · Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor · 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 0.95
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 7FD0 · PDBe 7FD0 · UniProt Q13546
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