MolNFT v1 · #103911 · protein
Crystal structure of spleen tyrosine kinase (syk) in complex with gs- 9973
4PUZ · Tyrosine-protein kinase syk: “Crystal structure of spleen tyrosine kinase (syk) in complex with gs- 9973”. X-ray diffraction, 1 ligand (CG9), 4 pockets (best druggability 0.72). MolNFT v1 #103911 on GenesisL1: 3D structure, binding…
- PDB
- 4PUZ
- Type
- protein
- Length
- 528 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
- CG9
- 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 | 40% helix, 24% strand | P43405 |
| B | Tyrosine-protein kinase syk (EC 2.7.10.2) | protein | 265 | 40% helix, 24% strand | P43405 |
Ligands and binding sites
- CG9 · 6-(1H-indazol-6-yl)-N-[4-(morpholin-4-yl)phenyl]imidazo[1,2-a]pyrazin-8-amine · ligand · 2 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 | 698 | 0.72 | 0.78 | 72 | CG9 |
| 2 | 393 | 0.63 | 0.78 | 39 | CG9 |
| 3 | 87 | 0.32 | 0.73 | 20 | empty |
| 4 | 80 | 0.31 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4PUZ · Crystal structure of spleen tyrosine kinase (Syk) in complex with GS-9973 · 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 0.92
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 4PUZ · PDBe 4PUZ · UniProt P43405
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