Research workbench
Crystal structure of JAK3 kinase domain in complex with an indazole substituted pyrrolopyrazine inhibitor
Analyse Crystal structure of JAK3 kinase domain in complex with an indazole substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZC6
- Type
- protein
- Length
- 1,103 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase JAK3
- EC
- 2.7.10.2, 2.7.1.112
- UniProt
- P52333
- Ligands
- VFC, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 279 | 43% helix, 20% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 278 | 43% helix, 21% strand | P52333 |
| C | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 277 | 44% helix, 20% strand | P52333 |
| D | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 269 | 44% helix, 20% strand | P52333 |
Ligands and binding sites
- VFC · N-[(2R)-1-(3-cyanoazetidin-1-yl)-1-oxidanylidene-propan-2-yl]-2-(6-fluoranyl-1-methyl-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.77 | 0.79 | 96 | VFC |
| 2 | 673 | 0.74 | 0.80 | 76 | VFC |
| 3 | 470 | 0.74 | 0.83 | 53 | VFC |
| 4 | 364 | 0.69 | 0.82 | 42 | VFC |
| 5 | 294 | 0.58 | 0.77 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 770 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 761 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 214 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 3ZC6 · Crystal structure of JAK3 kinase domain in complex with an indazole substituted… · the same entry in another collection · chain D against D, TM-score 1.00
- P52333 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase JAK3 (P52333) · a predicted model of the same protein · chain D 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 P52333
- Elsewhere: RCSB PDB 3ZC6 · PDBe 3ZC6 · UniProt P52333
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