Research workbench
Crystal structure of JAK3 in complex with FM587 (compound 9A)
Analyse Crystal structure of JAK3 in complex with FM587 (compound 9A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7APG
- Type
- protein
- Length
- 1,123 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
- UniProt
- P52333
- Ligands
- RQT, PHU
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 279 | 42% helix, 20% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 278 | 42% helix, 21% strand | P52333 |
| C | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 289 | 41% helix, 19% strand | P52333 |
| D | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 277 | 43% helix, 20% strand | P52333 |
Ligands and binding sites
- RQT · ~{N}-[3-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl) phenyl]propanamide · ligand · 4 copies · chains A, B, C, D
- PHU · 1-phenylurea · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.81 | 0.83 | 90 | RQT, EDO |
| 2 | 996 | 0.80 | 0.82 | 97 | empty |
| 3 | 81 | 0.76 | 0.98 | 18 | PHU |
| 4 | 67 | 0.76 | 0.99 | 17 | PHU |
| 5 | 934 | 0.75 | 0.78 | 78 | RQT, EDO |
Interfaces
5 interfaces between chains.
- A–C · 773 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 733 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7APG · Crystal structure of JAK3 in complex with FM587 (compound 9a) · 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 7APG · PDBe 7APG · UniProt P52333
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