3H3C: PYK2

Crystal structure of PYK2 in complex with Sulfoximine-substituted trifluoromethylpyrimidine analog. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 May 2009.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,219
Mol. weight: 33.13 kDa
Ligands: P1E
Released: 26 May 2009

Explore 3H3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H3C contains 17 α-helices and 9 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	422-424	3
β-strand	425-434	10	1
β-strand	437-445	9	1
β-strand	451-457	7	1
α-helix	465-480	16
β-strand	486	1	2
β-strand	489-493	5	1
β-strand	499-503	5	1
α-helix	504	1
β-strand	509	1	2
α-helix	510-516	7
α-helix	523-542	20
α-helix	545-547	3
α-helix	552-554	3
β-strand	555-559	5	2
β-strand	562-565	4	2
α-helix	589-591	3
α-helix	594-599	6
α-helix	604-619	16
α-helix	623-624	2
α-helix	631-639	9
α-helix	644-647	4
α-helix	652-661	10
α-helix	666-668	3
α-helix	670-671	2
α-helix	672-691	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein tyrosine kinase 2 beta	A	protein	277	Homo sapiens	Q14289 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3H3C_1 Protein tyrosine kinase 2 beta (chains A)
PQYGIAREDVVLNRILGEGFFGEVYEGVYTNHKGEKINVAVKTCKKDCTLDNKEKFMSEA
VIMKNLDHPHIVKLIGIIEEEPTWIIMELYPYGELGHYLERNKNSLKVLTLVLYSLQICK
AMAYLESINCVHRDIAVRNILVASPECVKLGDFGLSRYIEDEDYYKASVTRLPIKWMSPE
SINFRRFTTASDVWMFAVCMWEILSFGKQPFFWLENKDVIGVLEKGDRLPKPDLCPPVLY
TLMTRCWDYDPSDRPRFTELVCSLSDVYQMEKDIAME

Ligands and cofactors

ID	Name	Formula	Copies
P1E	4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidi…	C19 H25 F3 N6 O2 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Sulfoximine-substituted trifluoromethylpyrimidine analogs as inhibitors of proline-rich tyrosine kinase 2 (PYK2) show reduced hERG activity. Walker, D.P., Zawistoski, M.P., McGlynn, M.A. et al. Bioorg Med Chem Lett (2009) 19:3253-3258. DOI 10.1016/j.bmcl.2009.04.093 · PubMed

Other PDB entries of the same protein (UniProt Q14289 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CC6 1.6 Å, Crystal structure of kinase domain of protein tyrosine kinase 2 beta (PTK2B)
3FZS 1.75 Å, Crystal Structure of PYK2 complexed with BIRB796
4XEK 1.79 Å, Pyk2-FAT domain in complex with leupaxin LD4 motif
8XOX 1.9 Å, The Crystal Structure of FAK2 from Biortus.
3FZT 1.95 Å, Crystal structure of PYK2 complexed with PF-4618433
5TO8 1.98 Å, Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves…
4H1M 1.99 Å, Crystal structure of PYK2 with the indole 10c
4H1J 2.0 Å, Crystal structure of PYK2 with the pyrazole 13a
8YGX 2.0 Å, Structure of the PYK2 from Biortus.
4XEV 2.01 Å, Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide
3FZP 2.1 Å, Crystal structure of PYK2 complexed with ATPgS
5TOB 2.12 Å, Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves…

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