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
- 7FCZ
- Type
- protein
- Length
- 511 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
- 3IF
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 248 | 41% helix, 19% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 263 | 43% helix, 16% strand | Q13546 |
Ligands and binding sites
- 3IF · N-[(3S)-7-(2-cyclopropylethynyl)-5-methyl-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 | 1155 | 0.78 | 0.79 | 93 | empty |
| 2 | 341 | 0.72 | 0.84 | 39 | 3IF |
| 3 | 273 | 0.69 | 0.84 | 33 | 3IF |
| 4 | 77 | 0.41 | 0.79 | 21 | empty |
| 5 | 79 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7FCZ · 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 A 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 7FCZ · PDBe 7FCZ · UniProt Q13546
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