Research workbench
Human JAK1 kinase domain in complex with inhibitor
Analyse Human JAK1 kinase domain in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SM8
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase JAK1
- EC
- 2.7.10.2
- UniProt
- P23458
- Ligands
- LKT
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK1 (EC 2.7.10.2) | protein | 297 | 41% helix, 20% strand | P23458 |
| B | Tyrosine-protein kinase JAK1 (EC 2.7.10.2) | protein | 284 | 43% helix, 21% strand | P23458 |
Ligands and binding sites
- LKT · 2-chloranyl-6-[(3~{S})-3-[(1~{S})-2-cyano-1-[4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)pyrazol-1-yl]ethyl]pyrrolidin-1-yl]benzenecarbonitrile · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.67 | 0.84 | 32 | LKT |
| 2 | 246 | 0.65 | 0.83 | 37 | LKT |
| 3 | 134 | 0.56 | 0.83 | 27 | empty |
| 4 | 118 | 0.55 | 0.83 | 27 | empty |
| 5 | 106 | 0.38 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6SM8 · Human jak1 kinase domain in complex with inhibitor · 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 P23458
- Elsewhere: RCSB PDB 6SM8 · PDBe 6SM8 · UniProt P23458
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