MolNFT v1 · #82195 · protein
Crystal structure of spleen tyrosine kinase syk catalytic domain with pyrazolylbenzimidazole inhibitor 416
3VF8 · Tyrosine-protein kinase syk: “Crystal structure of spleen tyrosine kinase syk catalytic domain with pyrazolylbenzimidazole inhibitor 416”. X-ray diffraction, 1 ligand (0JE), 1 pocket (best druggability 0.62). MolNFT v1 #82195 on…
- PDB
- 3VF8
- Type
- protein
- Length
- 265 residues
- Chains
- 1
- 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
- 0JE
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% 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 |
Ligands and binding sites
- 0JE · 3-[5-(5-ethoxy-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]-1,1-diethylurea · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.62 | 0.78 | 48 | 0JE |
Compared structures
- 3VF8 · Crystal Structure of Spleen Tyrosine Kinase Syk Catalytic Domain with… · 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 3VF8 · PDBe 3VF8 · UniProt P43405
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