5LMA: Human spleen tyrosine kinase kinase domain

Human spleen tyrosine kinase kinase domain in complex with azanaphthyridine inhibitor. Determined by X-ray diffraction at 1.43 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 1.43 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,786
Mol. weight: 32.73 kDa
Ligands: 6ZG
Released: 14 Sept 2016

Explore 5LMA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LMA contains 16 α-helices and 13 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	367-369	3
β-strand	370-380	11	1
β-strand	383-391	9	1
β-strand	396-404	9	1
α-helix	406-408	3
α-helix	411-424	14
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	456-462	7
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
α-helix	519-520	2
β-strand	525-527	3	4
α-helix	536-538	3
α-helix	541-546	6
β-strand	548-550	3	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	619-630	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase SYK	A	protein	277	Homo sapiens	P43405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5LMA_1 Tyrosine-protein kinase SYK (chains A)
GPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELL
AEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQV
SMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKW
YAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCP
REMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN

Ligands and cofactors

ID	Name	Formula	Copies
6ZG	~{N}'-[7-(4-methylphenyl)pyrido[3,4-b]pyrazin-5-yl]butane-1,4-diamine	C18 H21 N5	1

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

Primary citation

Optimisation of a novel series of potent and orally bioavailable azanaphthyridine SYK inhibitors. Garton, N.S., Barker, M.D., Davis, R.P. et al. Bioorg Med Chem Lett (2016) 26:4606-4612. DOI 10.1016/j.bmcl.2016.08.070 · 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…
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
4PX6 1.6 Å, SYK catalytic domain in complex with a potent pyridopyrimidinone inhibitor

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