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Crystal structure of spleen tyrosine kinase syk catalytic domain with pyrazolylbenzimidazole inhibitor 416

Analyse Crystal structure of spleen tyrosine kinase syk catalytic domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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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