Research workbench
Crystal structure of spleen tyrosine kinase (syk) in complex with a diaminopyrimidine carboxamide inhibitor
Analyse Crystal structure of spleen tyrosine kinase (syk) in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SRV
- Type
- protein
- Length
- 526 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
- S19
- Pockets
- 4 · best druggability 0.72
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 | 263 | 41% helix, 22% strand | P43405 |
| B | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 263 | 40% helix, 25% strand | P43405 |
Ligands and binding sites
- S19 · 2-{[(3R,4R)-3-aminotetrahydro-2H-pyran-4-yl]amino}-4-[(4-methylphenyl)amino]pyrimidine-5-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.72 | 0.78 | 82 | S19, GOL |
| 2 | 412 | 0.65 | 0.78 | 46 | S19 |
| 3 | 97 | 0.33 | 0.73 | 19 | empty |
| 4 | 56 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3SRV · Crystal structure of spleen tyrosine kinase (SYK) in complex with a diaminopyrimidine… · the same entry in another collection · chain A against A, TM-score 1.00
- P43405 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase syk (P43405) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 3SRV · PDBe 3SRV · UniProt P43405
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