MolNFT v1 · #162323 · protein
Crystal structure of RIP1 kinase in complex with DHP77
6R5F · Receptor-interacting SERINE/THREONINE-protein kinase 1: “Crystal structure of RIP1 kinase in complex with DHP77”. X-ray diffraction, 1 ligand (JSW), 9 pockets (best druggability 0.76). MolNFT v1 #162323 on GenesisL1: 3D structure…
- PDB
- 6R5F
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- 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
- JSW
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 43% 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 | 252 | 46% helix, 13% strand | Q13546 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 256 | 45% helix, 16% strand | Q13546 |
| C | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 253 | 42% helix, 15% strand | Q13546 |
| D | Receptor-interacting SERINE/THREONINE-protein kinase 1 (EC 2.7.11.1) | protein | 250 | 40% helix, 14% strand | Q13546 |
Ligands and binding sites
- JSW · [(5~{S})-5-[3,5-bis(fluoranyl)phenyl]pyrazolidin-1-yl]-[1-(5-methyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl]methanone · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.76 | 0.78 | 82 | JSW |
| 2 | 812 | 0.76 | 0.80 | 77 | JSW |
| 3 | 293 | 0.74 | 0.86 | 36 | JSW |
| 4 | 319 | 0.71 | 0.84 | 44 | JSW |
| 5 | 227 | 0.50 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 905 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 827 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 134 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R5F · Crystal structure of RIP1 kinase in complex with DHP77 · the same entry in another collection · chain D against D, 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 6R5F · PDBe 6R5F · UniProt Q13546
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