Research workbench
JAK2 JH1 in complex with SY5-103
Analyse JAK2 JH1 in complex with SY5-103 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VNM
- Type
- protein
- Length
- 587 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
- R5Y
- Pockets
- 4 · 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 | 289 | 44% helix, 20% strand | O60674 |
| A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 298 | 43% helix, 20% strand | O60674 |
Ligands and binding sites
- R5Y · 4-[1-(but-3-en-1-yl)-1H-pyrazol-4-yl]-N-[4-(piperidin-4-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-2-amine · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.75 | 0.81 | 69 | empty |
| 2 | 510 | 0.70 | 0.80 | 61 | R5Y |
| 3 | 307 | 0.64 | 0.81 | 46 | R5Y |
| 4 | 68 | 0.39 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 471 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6VNM · JAK2 JH1 in complex with SY5-103 · 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 6VNM · PDBe 6VNM · UniProt O60674
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