6HM7: Spleen tyrosine kinase

Crystal structure of spleen tyrosine kinase (SYK) in complex with a 2-(phenoxymethyl)pyridine inhibitor. Determined by X-ray diffraction at 1.64 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,561
Mol. weight: 32.89 kDa
Ligands: GDH
Released: 10 Oct 2018

Explore 6HM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6HM7 contains 16 α-helices and 14 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	367-369	3
β-strand	370-372	3	1
β-strand	378-379	2	1
β-strand	383-391	9	1
β-strand	396-404	9	1
α-helix	411-426	16
β-strand	432	1	2
α-helix	433-434	2
β-strand	435-440	6	1
β-strand	444-449	6	1
β-strand	454-455	2	2
α-helix	456-461	6
α-helix	468-487	20
β-strand	490-491	2	3
α-helix	497-499	3
β-strand	500-504	5	2
β-strand	507-510	4	2
β-strand	517-518	2	3
β-strand	526-527	2	4
α-helix	536-538	3
α-helix	541-546	6
β-strand	548-549	2	4
α-helix	551-566	16
α-helix	570-571	2
α-helix	578-586	9
α-helix	593-594	2
α-helix	599-608	10
α-helix	613-615	3
α-helix	617-618	2
α-helix	619-632	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase SYK	A	protein	276	Homo sapiens	P43405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6HM7_1 Tyrosine-protein kinase SYK (chains A)
PKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLA
EANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVS
MGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWY
APECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPR
EMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN

Ligands and cofactors

ID	Name	Formula	Copies
GDH	7-[2-methoxy-6-[(4-methylpyridin-2-yl)methoxy]phenyl]-2,3,4,5-tetrahydro-1~{H}-…	C24 H26 N2 O2	1

Water and common crystallization additives (DMS, GOL, BR) are not listed.

Primary citation

Discovery of potent and selective Spleen Tyrosine Kinase inhibitors for the topical treatment of inflammatory skin disease. Barker, M.D., Liddle, J., Atkinson, F.L. et al. Bioorg Med Chem Lett (2018) 28:3458-3462. DOI 10.1016/j.bmcl.2018.09.022 · PubMed

Other PDB entries of the same protein (UniProt P43405 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YJR 1.32 Å, SYK kinase domain in complex with inhibitor GTC000225
4YJQ 1.34 Å, SYK kinase domain in complex with inhibitor GTC000224
4FYO 1.4 Å, Crystal structure of spleen tyrosine kinase complexed with…
5LMA 1.43 Å, Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine inhibitor
3BUW 1.45 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in Syk
6ZCS 1.47 Å, SYK Kinase domain in complex with azabenzimidazole inhibitor 3
5TIU 1.49 Å, Crystal structure of SYK kinase domain with inhibitor
8XQ1 1.5 Å, Crystal structure of spleen tyrosine kinase(SYK) in complex with SKI-G-1673
8BI2 1.51 Å, Syk kinase domain in complex with macrocyclic inhibitor 20a
4YJT 1.52 Å, The kinase domain of human spleen tyrosine (SYK) in complex with GTC000233
1XBB 1.57 Å, Crystal structure of the syk tyrosine kinase domain with Gleevec
4RX8 1.59 Å, SYK Catalytic Domain Complexed with a Potent Triazine Inhibitor2

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