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Crystal structure of spleen tyrosine kinase (syk) in complex with a 2- (PYRIDINYLOXYMETHYL)PYRIDINE inhibitor

Analyse Crystal structure of spleen tyrosine kinase (syk) in complex with a 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HM6
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spleen tyrosine kinase
UniProt: P43405
Ligands: GDK
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spleen tyrosine kinase	protein	261	41% helix, 22% strand	P43405

Ligands and binding sites

GDK · 2-(4-methylphenyl)-3-(pyridin-2-ylmethoxy)pyridine · ligand · chains A
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.65	0.79	37	GDK
2	75	0.31	0.74	16	empty

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

6HM6 · Crystal structure of spleen tyrosine kinase (syk) in complex with a… · 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 6HM6 · PDBe 6HM6 · UniProt P43405

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