MolNFT v1 · #162868 · protein
Crystal structure of RIP1 kinase in complex with GSK3145095
6RLN · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Crystal structure of RIP1 kinase in complex with GSK3145095”. X-ray diffraction, 1 ligand (K8K), 6 pockets (best druggability 0.76). MolNFT v1 #162868 on GenesisL1: 3D…
- PDB
- 6RLN
- Type
- protein
- Length
- 531 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
- K8K
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 266 | 40% helix, 15% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 265 | 42% helix, 15% strand | Q13546 |
Ligands and binding sites
- K8K · ~{N}-[(3~{S})-7,9-bis(fluoranyl)-2-oxidanylidene-1,3,4, 5-tetrahydro-1-benzazepin-3-yl]-3-(phenylmethyl)-1~{H}-1,2,4-triazole-5-carboxamide · 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 | 1153 | 0.76 | 0.79 | 85 | empty |
| 2 | 232 | 0.74 | 0.88 | 33 | K8K |
| 3 | 206 | 0.74 | 0.89 | 29 | K8K |
| 4 | 51 | 0.37 | 0.80 | 13 | empty |
| 5 | 79 | 0.33 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 427 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RLN · Crystal structure of RIP1 kinase in complex with GSK3145095 · 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 6RLN · PDBe 6RLN · UniProt Q13546
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