MolNFT v1 · #167516 · protein
JAK2 JH1 in complex with BL2-096
6VNC · Tyrosine-protein kinase JAK2: “JAK2 JH1 in complex with BL2-096”. X-ray diffraction, 1 ligand (R6V), 5 pockets (best druggability 0.77). MolNFT v1 #167516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VNC
- Type
- protein
- Length
- 586 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
- R6V
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 289 | 41% helix, 20% strand | O60674 |
| A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 297 | 42% helix, 21% strand | O60674 |
Ligands and binding sites
- R6V · (3R)-3-cyclopentyl-3-[4-(2-{[4-(piperidin-4-yl) phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.77 | 0.84 | 63 | empty |
| 2 | 411 | 0.71 | 0.82 | 50 | R6V |
| 3 | 419 | 0.70 | 0.81 | 51 | R6V |
| 4 | 78 | 0.41 | 0.79 | 15 | empty |
| 5 | 70 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 469 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, covalent ligand).
Compared structures
- 6VNC · JAK2 JH1 in complex with BL2-096 · 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 6VNC · PDBe 6VNC · UniProt O60674
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