MolNFT v1 · #95549 · protein
Crystal structure of RIP1 kinase in complex with necrostatin-1 analog
4ITH · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Crystal structure of RIP1 kinase in complex with necrostatin-1 analog”. X-ray diffraction, 3 ligands (RCM, NA, IOD), 7 pockets (best druggability 0.78). MolNFT v1 #95549 on…
- PDB
- 4ITH
- Type
- protein
- Length
- 517 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
- RCM, NA, IOD
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 247 | 42% helix, 15% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 270 | 41% helix, 16% strand | Q13546 |
Ligands and binding sites
- RCM · (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.97 | 18 | RCM |
| 2 | 96 | 0.77 | 0.97 | 18 | RCM |
| 3 | 280 | 0.51 | 0.74 | 23 | IOD |
| 4 | 152 | 0.41 | 0.74 | 18 | IOD |
| 5 | 60 | 0.31 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 128 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ITH · Crystal structure of RIP1 kinase in complex with necrostatin-1 analog · 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 0.96
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 Q13546
- Elsewhere: RCSB PDB 4ITH · PDBe 4ITH · UniProt Q13546
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