6N7D: Human JAK1 kinase domain with compound 54

Structure of the human JAK1 kinase domain with compound 54. Determined by X-ray diffraction at 1.78 Å resolution. Released 24 Apr 2019.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,532
Mol. weight: 35.21 kDa
Ligands: KF4
Released: 24 Apr 2019

Explore 6N7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6N7D contains 17 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: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	869	1	1
α-helix	872-874	3
β-strand	875-883	9	1
β-strand	887-894	8	1
β-strand	903-910	8	1
α-helix	919-930	12
β-strand	937	1	2
α-helix	938-939	2
β-strand	940-944	5	1
β-strand	953-957	5	1
β-strand	963	1	2
α-helix	964-970	7
α-helix	977-996	20
β-strand	999-1000	2	3
α-helix	1006-1008	3
β-strand	1009-1013	5	2
β-strand	1016-1019	4	2
β-strand	1026-1027	2	3
α-helix	1028-1029	2
β-strand	1034-1036	3	4
α-helix	1045-1047	3
α-helix	1050-1055	6
β-strand	1057-1059	3	4
α-helix	1060-1075	16
α-helix	1080-1082	3
α-helix	1084-1092	9
α-helix	1097-1099	3
α-helix	1100-1109	10
α-helix	1114-1117	4
α-helix	1122-1131	10
α-helix	1142-1153	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein kinase JAK1	A	protein	302	Homo sapiens	P23458 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6N7D_1 Tyrosine-protein kinase JAK1 (chains A)
GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKP
ESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNK
NKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDK
EYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMI
GPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEAL
LK

Ligands and cofactors

ID	Name	Formula	Copies
KF4	N-[5-(6-methoxy-1H-indazol-5-yl)-1H-pyrazol-4-yl]pyrazolo[1,5-a]pyrimidine-3-ca…	C18 H14 N8 O2	1

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

Primary citation

Discovery of a class of highly potent Janus Kinase 1/2 (JAK1/2) inhibitors demonstrating effective cell-based blockade of IL-13 signaling. Zak, M., Hanan, E.J., Lupardus, P. et al. Bioorg Med Chem Lett (2019) 29:1522-1531. DOI 10.1016/j.bmcl.2019.04.008 · PubMed

Other PDB entries of the same protein (UniProt P23458 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6N7A 1.33 Å, Structure of the human JAK1 kinase domain with compound 39
10PI 1.54 Å, JAK1 kinase (JH1 domain) in complex with povorcitinib
6N77 1.64 Å, Structure of the human JAK1 kinase domain with compound 15
6N7C 1.69 Å, Structure of the human JAK1 kinase domain with compound 56
6GGH 1.7 Å, Human jak1 kinase domain in complex with inhibitor
6RSH 1.71 Å, Structure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole…
8S85 1.75 Å, Crystal structure of JAK1 JH1 domain in complex with an inhibitor
6RSD 1.76 Å, Structure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole…
4GS0 1.8 Å, Crystal structure of SHP1 catalytic domain with JAK1 activation loop peptide
4L00 1.8 Å, Crystal structure of the apo Jak1 pseudokinase domain
6ELR 1.8 Å, Human jak1 kinase domain in complex with compound 7
6RSB 1.8 Å, Structure based optimization of JAK1-ATP binding pocket Inhibitors in the aminopyrazole…

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