Research workbench
Crystal structure of tyrosine kinase 2 JH2 (pseudo kinase domain) complexed with COMPOUND_29 aka 6-[(5-fluoro-4-meth ylpyridin-2-yl) amino]-4-({2-methoxy-3-[(pyridin-2-ylmethyl )CARBAMOYL]PHENYL}AMINO)- N-methylpyridine-3-carboxamide
Analyse Crystal structure of tyrosine kinase 2 JH2 (pseudo kinase domain) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NZQ
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-receptor tyrosine-protein kinase TYK2
- EC
- 2.7.10.2
- UniProt
- P29597
- Ligands
- LB4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-receptor tyrosine-protein kinase TYK2 (EC 2.7.10.2) | protein | 256 | 39% helix, 20% strand | P29597 |
| B | Non-receptor tyrosine-protein kinase TYK2 (EC 2.7.10.2) | protein | 258 | 40% helix, 20% strand | P29597 |
Ligands and binding sites
- LB4 · 6-[(5-fluoro-4-methylpyridin-2-yl)amino]-4-[(2-methoxy-3-{[(pyridin-2-yl)methyl]carbamoyl}phenyl)amino]-N-methylpyridine-3-carboxamide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.72 | 0.78 | 72 | LB4 |
| 2 | 389 | 0.68 | 0.81 | 42 | LB4 |
| 3 | 95 | 0.44 | 0.79 | 21 | empty |
| 4 | 88 | 0.34 | 0.74 | 18 | empty |
| 5 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6NZQ · CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN) COMPLEXED WITH… · 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 P29597
- Elsewhere: RCSB PDB 6NZQ · PDBe 6NZQ · UniProt P29597
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