8BI2: Syk kinase domain

Syk kinase domain in complex with macrocyclic inhibitor 20a. Determined by X-ray diffraction at 1.51 Å resolution. Released 14 Jun 2023.

Method: X-ray diffraction
Resolution: 1.51 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,284
Mol. weight: 35.34 kDa
Ligands: QR7
Released: 14 Jun 2023

Explore 8BI2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BI2 contains 16 α-helices and 15 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	364	1	1
α-helix	367-369	3
β-strand	370-372	3	1
β-strand	378-379	2	1
β-strand	384-391	8	1
β-strand	396-403	8	1
α-helix	414-426	13
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	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	591-594	4
α-helix	599-608	10
α-helix	613-615	3
α-helix	619-636	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase SYK	A	protein	299	Homo sapiens	P43405 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8BI2_1 Tyrosine-protein kinase SYK (chains A)
MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVK
ILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQ
NRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRAD
ENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVT
AMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
QR7	10,13,23-trimethyl-16-oxa-2,4,8,9,13,19,23,30-octazapentacyclo[19.5.2.1^{3,7}.1…	C24 H28 N8 O2	1

Primary citation

Optimization of a series of novel, potent and selective Macrocyclic SYK inhibitors. Grimster, N.P., Gingipalli, L., Balazs, A. et al. Bioorg Med Chem Lett (2023) 91:129352-129352. DOI 10.1016/j.bmcl.2023.129352 · 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
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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