MolNFT v1 · #164489 · protein
RIP2 kinase catalytic domain complex with 5AMINO1TERTBUTYL3(3METHOXYPHENYL)1H PYRAZOLE4CARBOXAMIDE.
6SZJ · Receptor-interacting SERINE/THREONINE-protein kinase 2: “RIP2 kinase catalytic domain complex with 5AMINO1TERTBUTYL3(3METHOXYPHENYL)1H PYRAZOLE4CARBOXAMIDE.”. X-ray diffraction, 2 ligands (M5W, CA), 6 pockets (best druggability…
- PDB
- 6SZJ
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-interacting SERINE/THREONINE-protein kinase 2
- EC
- 2.7.11.1
- UniProt
- O43353
- Ligands
- M5W, CA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 279 | 39% helix, 16% strand | O43353 |
| B | Receptor-interacting SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 283 | 40% helix, 17% strand | O43353 |
Ligands and binding sites
- M5W · 5-amino-1-~{tert}-butyl-3-(3-methoxyphenyl)pyrazole-4-carboxamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains 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 | 1129 | 0.81 | 0.82 | 69 | empty |
| 2 | 496 | 0.71 | 0.81 | 56 | M5W |
| 3 | 266 | 0.65 | 0.82 | 30 | M5W |
| 4 | 144 | 0.44 | 0.76 | 27 | empty |
| 5 | 103 | 0.43 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1958 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6SZJ · RIP2 Kinase Catalytic Domain complex with 5amino1tertbutyl3(3methoxyphenyl)1H… · the same entry in another collection · chain A against A, TM-score 1.00
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 6SZJ · PDBe 6SZJ · UniProt O43353
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