MolNFT v1 · #113829 · protein
RIP2 kinase catalytic domain (1 - 310) complex with sb-203580
5AR4 · Receptor-interacting SERINE/THREONINE-protein kinase 2: “RIP2 kinase catalytic domain (1 - 310) complex with sb-203580”. X-ray diffraction, 1 ligand (SB2), 5 pockets (best druggability 0.83). MolNFT v1 #113829 on GenesisL1: 3D…
- PDB
- 5AR4
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 2
- EC
- 2.7.10.2, 2.7.11.1
- UniProt
- O43353
- Ligands
- SB2
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 274 | 41% helix, 17% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 279 | 41% helix, 17% strand | O43353 |
Ligands and binding sites
- SB2 · 4-[5-(4-fluoro-phenyl)-2-(4-methanesulfinyl-phenyl)-3H-imidazol-4-yl]-pyridine · 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 | 1139 | 0.83 | 0.84 | 94 | empty |
| 2 | 201 | 0.65 | 0.84 | 27 | SB2 |
| 3 | 249 | 0.63 | 0.81 | 28 | SB2 |
| 4 | 94 | 0.40 | 0.77 | 22 | empty |
| 5 | 58 | 0.35 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1906 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5AR4 · RIP2 Kinase Catalytic Domain (1 - 310) complex with SB-203580 · the same entry in another collection · chain A against A, TM-score 1.00
- O43353 · AlphaFold monomer V2.0 prediction for receptor-interacting SERINE/THREONINE-protein… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O43353
- Elsewhere: RCSB PDB 5AR4 · PDBe 5AR4 · UniProt O43353
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