MolNFT v1 · #167519 · protein
JAK2 JH1 in complex with MA9-086
6VNF · Tyrosine-protein kinase JAK2: “JAK2 JH1 in complex with MA9-086”. X-ray diffraction, 1 ligand (R6S), 5 pockets (best druggability 0.75). MolNFT v1 #167519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VNF
- Type
- protein
- Length
- 589 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
- R6S
- Pockets
- 5 · best druggability 0.75
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 | 291 | 44% helix, 19% strand | O60674 |
| A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 298 | 42% helix, 20% strand | O60674 |
Ligands and binding sites
- R6S · N~4~-[1-(tert-butylsulfonyl)-2,3-dihydro-1H-indol-6-yl]-N~2~-[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]-5-methylpyrimidine-2,4-diamine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.75 | 0.81 | 62 | empty |
| 2 | 447 | 0.73 | 0.83 | 49 | R6S |
| 3 | 272 | 0.64 | 0.81 | 31 | R6S |
| 4 | 118 | 0.57 | 0.84 | 25 | empty |
| 5 | 79 | 0.40 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 510 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6VNF · JAK2 JH1 in complex with MA9-086 · 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 6VNF · PDBe 6VNF · UniProt O60674
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