MolNFT v1 · #113830 · protein
RIP2 kinase catalytic domain (1 - 310) complex with benzimidazole
5AR5 · Receptor-interacting SERINE/THREONINE-protein kinase 2: “RIP2 kinase catalytic domain (1 - 310) complex with benzimidazole”. X-ray diffraction, 2 ligands (IQ7, CA), 7 pockets (best druggability 0.80). MolNFT v1 #113830 on GenesisL1…
- PDB
- 5AR5
- Type
- protein
- Length
- 563 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
- IQ7, CA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% 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 | 284 | 38% helix, 18% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.10.2, 2.7.11.1) | protein | 279 | 39% helix, 18% strand | O43353 |
Ligands and binding sites
- IQ7 · 2-(2-(4-chlorophenyl)-1H-imidazol-5-yl)-N,1-bis(2-methoxyethyl)-1H-benzo[d]imidazole-5-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
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 | 1200 | 0.80 | 0.81 | 79 | empty |
| 2 | 428 | 0.72 | 0.82 | 55 | IQ7 |
| 3 | 245 | 0.68 | 0.84 | 33 | IQ7 |
| 4 | 112 | 0.42 | 0.76 | 19 | empty |
| 5 | 92 | 0.37 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1869 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5AR5 · RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole · 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 B against A, TM-score 0.97
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 5AR5 · PDBe 5AR5 · UniProt O43353
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