MolNFT v1 · #167525 · protein
JAK2 JH1 in complex with SG3-179
6VNL · Tyrosine-protein kinase JAK2: “JAK2 JH1 in complex with SG3-179”. X-ray diffraction, 1 ligand (5W2), 11 pockets (best druggability 0.76). MolNFT v1 #167525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VNL
- Type
- protein
- Length
- 1,175 residues
- Chains
- 4
- 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
- 5W2
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 289 | 44% helix, 19% strand | O60674 |
| B, A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 298 | 43% helix, 21% strand | O60674 |
| C | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 290 | 43% helix, 19% strand | O60674 |
Ligands and binding sites
- 5W2 · 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide · ligand · 4 copies · chains D, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.76 | 0.82 | 68 | empty |
| 2 | 458 | 0.76 | 0.85 | 58 | empty |
| 3 | 571 | 0.75 | 0.82 | 55 | 5W2 |
| 4 | 388 | 0.74 | 0.84 | 53 | 5W2 |
| 5 | 596 | 0.73 | 0.80 | 53 | 5W2 |
Interfaces
3 interfaces between chains.
- B–A · 1101 Ų buried · 16 hydrogen bonds · protein-protein
- D–B · 520 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 491 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6VNL · JAK2 JH1 in complex with SG3-179 · the same entry in another collection · chain D against D, 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 6VNL · PDBe 6VNL · UniProt O60674
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