5HEZ | pdb_00005hez

JAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209

• PDB DOI: https://doi.org/10.2210/pdb5HEZ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-01-06 Released: 2016-11-09 
• Deposition Author(s): Ultsch, M., Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.238 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity.

Dendrou, C.A., Cortes, A., Shipman, L., Evans, H.G., Attfield, K.E., Jostins, L., Barber, T., Kaur, G., Kuttikkatte, S.B., Leach, O.A., Desel, C., Faergeman, S.L., Cheeseman, J., Neville, M.J., Sawcer, S., Compston, A., Johnson, A.R., Everett, C., Bell, J.I., Karpe, F., Ultsch, M., Eigenbrot, C., McVean, G., Fugger, L.

(2016) Sci Transl Med 8: 363ra149-363ra149

• PubMed: 27807284 
• DOI: https://doi.org/10.1126/scitranslmed.aag1974
• Primary Citation Related Structures: 
  5HEZ


• PubMed Abstract: 
  

  Thousands of genetic variants have been identified, which contribute to the development of complex diseases, but determining how to elucidate their biological consequences for translation into clinical benefit is challenging. Conflicting evidence regarding the functional impact of genetic variants in the tyrosine kinase 2 (TYK2) gene, which is differentially associated with common autoimmune diseases, currently obscures the potential of TYK2 as a therapeutic target. We aimed to resolve this conflict by performing genetic meta-analysis across disorders; subsequent molecular, cellular, in vivo, and structural functional follow-up; and epidemiological studies. Our data revealed a protective homozygous effect that defined a signaling optimum between autoimmunity and immunodeficiency and identified TYK2 as a potential drug target for certain common autoimmune disorders.

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Organizational Affiliation: 
• Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
Department of Clinical Medicine, Aarhus University Hospital, 8200 Aarhus N, Denmark.
Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford OX3 7LE, UK.
National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Churchill Hospital, Oxford OX3 7LE, UK.
Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK.
Structural Biology and Biochemical Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
University of Oxford, Richard Doll Building, Roosevelt Drive, Oxford OX3 7DG, UK.
Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 146.16 kDa 
• Atom Count: 10,024 
• Modeled Residue Count: 1,162 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A, B, C, D	302	Homo sapiens	Mutation(s): 1  Gene Names: JAK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674  Go to UniProtKB:  O60674
PHAROS:  O60674 GTEx:  ENSG00000096968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1M3	G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D]	N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide C26 H35 N7 O2 S JVDOKQYTTYUYDV-UHFFFAOYSA-N
ZN	F [auth A], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], I [auth B], O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B, C, D	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
1M3	BindingDB:  5HEZ	IC50: min: 1.4, max: 97.6 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.238 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 211.813	α = 90
b = 215.649	β = 90
c = 91.497	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Ultsch, M., Eigenbrot, C.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary