6VNS: TYK2 kinase with compound 13

Crystal structure of TYK2 kinase with compound 13. Determined by X-ray diffraction at 2.09 Å resolution. Released 8 Apr 2020.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,541
Mol. weight: 36.96 kDa
Ligands: R5D
Released: 8 Apr 2020

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

Secondary structure: helices and β-sheets

6VNS contains 18 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	891	1	1
α-helix	894-896	3
β-strand	897-905	9	1
β-strand	909-916	8	1
β-strand	925-932	8	1
α-helix	938-953	16
β-strand	959	1	2
α-helix	960-961	2
β-strand	962-968	7	1
β-strand	973-979	7	1
β-strand	985	1	2
α-helix	986-989	4
α-helix	990-992	3
α-helix	997-1016	20
β-strand	1019-1020	2	3
α-helix	1026-1028	3
β-strand	1029-1033	5	2
β-strand	1036-1039	4	2
β-strand	1046-1047	2	3
α-helix	1048-1049	2
β-strand	1054-1056	3	4
α-helix	1065-1067	3
α-helix	1070-1075	6
β-strand	1077-1079	3	4
α-helix	1080-1095	16
α-helix	1100-1102	3
α-helix	1104-1112	9
α-helix	1120-1129	10
α-helix	1134-1137	4
α-helix	1142-1151	10
α-helix	1156-1158	3
α-helix	1162-1177	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-receptor tyrosine-protein kinase TYK2	A	protein	318	Homo sapiens	P29597 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VNS_1 Non-receptor tyrosine-protein kinase TYK2 (chains A)
MAHHHHHHHHHHGALEVLFQGPGDPTVFHKRYLKKIRDLGEGHFGKVSLYCYDPTNDGTG
EMVAVKALKADAGPQHRSGWKQEIDILRTLYHEHIIKYKGCCEDAGAASLQLVMEYVPLG
SLRDYLPRHSIGLAQLLLFAQQICEGMAYLHSQHYIHRDLAARNVLLDNDRLVKIGDFGL
AKAVPEGHEYYRVREDGDSPVFWYAPECLKEYKFYYASDVWSFGVTLYELLTHCDSSQSP
PTKFLELIGIAQGQMTVLRLTELLERGERLPRPDKCPAEVYHLMKNCWETEASFRPTFEN
LIPILKTVHEKYQGQAPS

Ligands and cofactors

ID	Name	Formula	Copies
R5D	(1R,2R)-2-cyano-N-[(1S,5R)-3-(5-fluoro-2-{[1-(2-hydroxyethyl)-1H-pyrazol-4-yl]a…	C19 H21 F N8 O2	1

Primary citation

Design and optimization of a series of 4-(3-azabicyclo[3.1.0]hexan-3-yl)pyrimidin-2-amines: Dual inhibitors of TYK2 and JAK1. Fensome, A., Ambler, C.M., Arnold, E. et al. Bioorg Med Chem (2020) 28:115481-115481. DOI 10.1016/j.bmc.2020.115481 · PubMed

Other PDB entries of the same protein (UniProt P29597 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3LXP 1.65 Å, Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in…
8S99 1.71 Å, Crystal structure of the TYK2 pseudokinase domain in complex with compound 11
4WOV 1.8 Å, Crystal structure of tyrosine kinase 2 JH2 (pseudo kinase domain) complexed with bms-066…
8S9A 1.83 Å, Crystal structure of the TYK2 pseudokinase domain in complex with TAK-279
8S98 1.87 Å, Crystal structure of the TYK2 pseudokinase domain in complex with compound 8
5C03 1.9 Å, Crystal Structure of kinase
5TKD 1.92 Å, Crystal structure of tyrosine kinase 2 JH2 (pseudo kinase domain) complexed with…
6NZE 1.96 Å, Crystal structure of tyrosine kinase 2 JH2 (pseudo kinase domain) complexed with…
8TB6 1.96 Å, TYK2 JH2 bound to Compound14
6AAM 1.98 Å, Crystal structure of TYK2 in complex with peficitinib
4PO6 1.99 Å, Crystal structure of the human TYK2 FERM and SH2 domains with an IFNAR1 intracellular…
3NZ0 2.0 Å, Non-phosphorylated TYK2 kinase with CMP6

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