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Crystal structure of JAK3 kinase domain in complex with a pyrrolopyrazine-2-phenyl ether inhibitor
Analyse Crystal structure of JAK3 kinase domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZEP
- Type
- protein
- Length
- 1,098 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
- 1NX
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 276 | 42% helix, 19% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 270 | 44% helix, 19% strand | P52333 |
| C | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 278 | 43% helix, 18% strand | P52333 |
| D | Tyrosine-protein kinase JAK3 (EC 2.7.10.2, 2.7.1.112) | protein | 274 | 43% helix, 19% strand | P52333 |
Ligands and binding sites
- 1NX · 2-[[(3R)-3-acetamido-2,3-dihydro-1H-inden-5-yl]oxy]-N-[(1S)-1-cyclopropylethyl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.78 | 0.80 | 80 | 1NX |
| 2 | 896 | 0.74 | 0.78 | 80 | 1NX |
| 3 | 231 | 0.65 | 0.83 | 30 | 1NX |
| 4 | 326 | 0.65 | 0.80 | 32 | empty |
| 5 | 345 | 0.61 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 805 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 800 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 3ZEP · Crystal Structure of JAK3 Kinase Domain in Complex with a Pyrrolopyrazine-2-phenyl Ether… · 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 3ZEP · PDBe 3ZEP · UniProt P52333
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