Research workbench
Crystal structure of JAK2-V617F pseudokinase domain in complex with compound 2
Analyse Crystal structure of JAK2-V617F pseudokinase domain in complex with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G3C
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase
- EC
- 2.7.10.2
- UniProt
- Q506Q0
- Ligands
- EKT
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 272 | 43% helix, 21% strand | Q506Q0 |
| B | Tyrosine-protein kinase (EC 2.7.10.2) | protein | 268 | 42% helix, 21% strand | Q506Q0 |
Ligands and binding sites
- EKT · 2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7,7-trimethyl-8-(3-methylbutyl)pteridin-6-one · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B
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 | 704 | 0.74 | 0.80 | 68 | EDO |
| 2 | 383 | 0.71 | 0.83 | 40 | EKT, EDO |
| 3 | 434 | 0.71 | 0.82 | 44 | EKT, EDO |
| 4 | 96 | 0.45 | 0.79 | 19 | empty |
| 5 | 93 | 0.43 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 522 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6G3C · Crystal Structure of JAK2-V617F pseudokinase domain in complex with Compound 2 · the same entry in another collection · chain A against A, 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 Q506Q0
- Elsewhere: RCSB PDB 6G3C · PDBe 6G3C · UniProt Q506Q0
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