MolNFT v1 · #167522 · protein
JAK2 JH1 in complex with PN3-115
6VNI · Tyrosine-protein kinase JAK2: “JAK2 JH1 in complex with PN3-115”. X-ray diffraction, 1 ligand (R61), 6 pockets (best druggability 0.71). MolNFT v1 #167522 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VNI
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase JAK2
- EC
- 2.7.10.2
- UniProt
- O60674
- Ligands
- R61
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 289 | 44% helix, 20% strand | O60674 |
| A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 291 | 44% helix, 21% strand | O60674 |
Ligands and binding sites
- R61 · 2-{5-[(2-{[3,5-difluoro-4-(1-methylpiperidin-4-yl) phenyl]amino}-5-methylpyrimidin-4-yl)amino]-2-fluorophenyl}-1lambda~6~,2-thiazolidine-1,1-dione · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.71 | 0.81 | 49 | R61 |
| 2 | 424 | 0.70 | 0.82 | 45 | R61 |
| 3 | 344 | 0.68 | 0.82 | 40 | empty |
| 4 | 287 | 0.61 | 0.79 | 24 | empty |
| 5 | 74 | 0.38 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 477 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6VNI · JAK2 JH1 in complex with PN3-115 · the same entry in another collection · chain B against B, 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 O60674
- Elsewhere: RCSB PDB 6VNI · PDBe 6VNI · UniProt O60674
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