Research workbench
Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine inhibitor
Analyse Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LMB
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase syk
- EC
- 2.7.10.2
- UniProt
- P43405
- Ligands
- 6ZF
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 265 | 40% helix, 23% strand | P43405 |
| B | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 262 | 39% helix, 25% strand | P43405 |
Ligands and binding sites
- 6ZF · 7-[6-(dimethylamino)pyridin-3-yl]-~{N}-[[(3~{S})-piperidin-3-yl]methyl]pyrido[3,4-b]pyrazin-5-amine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 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 | 566 | 0.68 | 0.78 | 63 | 6ZF, GOL |
| 2 | 283 | 0.62 | 0.80 | 36 | 6ZF |
| 3 | 229 | 0.54 | 0.77 | 33 | GOL |
| 4 | 98 | 0.34 | 0.73 | 19 | empty |
| 5 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 580 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5LMB · Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine 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 P43405
- Elsewhere: RCSB PDB 5LMB · PDBe 5LMB · UniProt P43405
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