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Crystal structure of syk in complex with gs-9876

Analyse Crystal structure of syk in complex with gs-9876 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VOV
Type: protein
Length: 522 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: R6D
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase syk (EC 2.7.10.2)	protein	258	40% helix, 26% strand	P43405
B	Tyrosine-protein kinase syk (EC 2.7.10.2)	protein	264	41% helix, 24% strand	P43405

Ligands and binding sites

R6D · 6-(6-aminopyrazin-2-yl)-N-{4-[4-(oxetan-3-yl)piperazin-1-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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	616	0.70	0.78	69	R6D
2	282	0.62	0.79	33	R6D
3	81	0.33	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 601 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6VOV · Crystal structure of Syk in complex with GS-9876 · 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 6VOV · PDBe 6VOV · UniProt P43405

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