MolNFT v1 · #167520 · protein
JAK2 JH1 in complex with PN2-118
6VNG · Tyrosine-protein kinase JAK2: “JAK2 JH1 in complex with PN2-118”. X-ray diffraction, 1 ligand (R6M), 4 pockets (best druggability 0.71). MolNFT v1 #167520 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VNG
- Type
- protein
- Length
- 581 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
- R6M
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 289 | 43% helix, 19% strand | O60674 |
| A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 292 | 43% helix, 21% strand | O60674 |
Ligands and binding sites
- R6M · N-{2-fluoro-5-[(2-{[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]amino}-5-methylpyrimidin-4-yl)amino]phenyl}-2-methylpropane-2-sulfonamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.71 | 0.80 | 51 | R6M |
| 2 | 455 | 0.71 | 0.82 | 59 | R6M |
| 3 | 338 | 0.69 | 0.83 | 38 | empty |
| 4 | 214 | 0.57 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- B–A · 466 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6VNG · JAK2 JH1 in complex with PN2-118 · 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 6VNG · PDBe 6VNG · UniProt O60674
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