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Syk kinase domain in complex with inhibitor GTC000225

Analyse Syk kinase domain in complex with inhibitor GTC000225 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YJR
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: 4DJ
Pockets: 3 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase syk (EC 2.7.10.2)	protein	265	38% helix, 23% strand	P43405

Ligands and binding sites

4DJ · 3-(1H-indazol-4-yl{2-[(1-methyl-1H-indazol-5-yl)amino]pyrimidin-4-yl}amino)propan-1-ol · ligand · chains A

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

Pockets

3 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	201	0.61	0.81	23	4DJ
2	62	0.31	0.75	21	empty
3	58	0.28	0.74	17	empty

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

4YJR · SYK kinase domain in complex with inhibitor GTC000225 · 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 4YJR · PDBe 4YJR · UniProt P43405

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