MolNFT v1 · #119867 · protein

Crystal structure of an inhibitor-bound syk

5GHV · Tyrosine-protein kinase syk: “Crystal structure of an inhibitor-bound syk”. X-ray diffraction, 1 ligand (X5G), 5 pockets (best druggability 0.70). MolNFT v1 #119867 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GHV
Type: protein
Length: 530 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: X5G
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tyrosine-protein kinase syk (EC 2.7.10.2)	protein	265	37% helix, 21% strand	P43405

Ligands and binding sites

X5G · 1-({1-[2-({3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]-4-methyl-1H-pyrrol-3-yl}methyl)azetidin-3-ol · ligand · 2 copies · chains A, B

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

Pockets

5 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	694	0.70	0.77	72	X5G
2	391	0.66	0.79	41	X5G
3	72	0.40	0.79	18	empty
4	73	0.32	0.74	19	empty
5	61	0.30	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 782 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5GHV · Crystal structure of an inhibitor-bound Syk · 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 5GHV · PDBe 5GHV · UniProt P43405

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