MolNFT v1 · #158505 · protein
Structure of human RIPK1 kinase domain in complex with compound 11
6NW2 · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Structure of human RIPK1 kinase domain in complex with compound 11”. X-ray diffraction, 1 ligand (L4Y), 4 pockets (best druggability 0.76). MolNFT v1 #158505 on GenesisL1: 3D…
- PDB
- 6NW2
- Type
- protein
- Length
- 506 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
- L4Y
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 260 | 44% helix, 15% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 246 | 44% helix, 13% strand | Q13546 |
Ligands and binding sites
- L4Y · (5R)-5-methyl-N-[(3S)-5-methyl-4-oxo-2,3,4,5-tetrahydro-1,5-benzoxazepin-3-yl]-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.76 | 0.79 | 88 | empty |
| 2 | 230 | 0.72 | 0.87 | 34 | L4Y |
| 3 | 199 | 0.72 | 0.88 | 33 | L4Y |
| 4 | 103 | 0.35 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NW2 · Structure of human RIPK1 kinase domain in complex with compound 11 · 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 6NW2 · PDBe 6NW2 · UniProt Q13546
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