MolNFT v1 · #111787 · protein
Crystal structure of the JAK3 kinase domain covalently bound to N-(3- (((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-YL)PHENYL)AMINO) pyrimidin-4-YL)AMINO)METHYL)PHENYL)ACRYLAMIDE
4Z16 · Tyrosine-protein kinase JAK3: “Crystal structure of the JAK3 kinase domain covalently bound to N-(3…”. X-ray diffraction, 1 ligand (4LH), 8 pockets (best druggability 0.72). MolNFT v1 #111787 on GenesisL1: 3D structure, binding…
- PDB
- 4Z16
- Type
- protein
- Length
- 1,097 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
- 4LH
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 273 | 42% helix, 20% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 278 | 42% helix, 20% strand | P52333 |
Ligands and binding sites
- 4LH · N-(3-{[(5-chloro-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]methyl}phenyl)prop-2-enamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.72 | 0.80 | 47 | 4LH |
| 2 | 554 | 0.69 | 0.78 | 68 | 4LH |
| 3 | 443 | 0.67 | 0.79 | 43 | 4LH |
| 4 | 417 | 0.66 | 0.79 | 43 | 4LH |
| 5 | 366 | 0.64 | 0.79 | 34 | empty |
Interfaces
2 interfaces between chains.
- A–D · 767 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 688 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 4 covalent (phosphorylation, covalent ligand).
Compared structures
- 4Z16 · Crystal Structure of the Jak3 Kinase Domain Covalently Bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P52333 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase JAK3 (P52333) · a predicted model of the same protein · chain A 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 4Z16 · PDBe 4Z16 · UniProt P52333
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