Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.72 kDa 
• Atom Count: 2,485 
• Modelled Residue Count: 287 
• Deposited Residue Count: 302 
• Unique protein chains: 1

 3NYX

Non-phosphorylated TYK2 JH1 domain with Quinoline-Thiadiazole-Thiophene Inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb3NYX/pdb

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


• Deposited: 2010-07-15 Released: 2010-10-20 
• Deposition Author(s): Eigenbrot, C., Ultsch, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 

Literature

A new regulatory switch in a JAK protein kinase.

Tsui, V., Gibbons, P., Ultsch, M., Mortara, K., Chang, C., Blair, W., Pulk, R., Stanley, M., Starovasnik, M., Williams, D., Lamers, M., Leonard, P., Magnuson, S., Liang, J., Eigenbrot, C.

(2011) Proteins 79: 393-401

• PubMed: 21117080 
• DOI: https://doi.org/10.1002/prot.22889
• Primary Citation of Related Structures:  
  3NYX, 3NZ0


• PubMed Abstract: 
  

Members of the JAK family of protein kinases mediate signal transduction from cytokine receptors to transcription factor activation. Over-stimulation of these pathways is causative in immune disorders like rheumatoid arthritis, psoriasis, lupus, and Crohn's disease. A search for selective inhibitors of a JAK kinase has led to our characterization of a previously unknown kinase conformation arising from presentation of Tyr962 of TYK2 to an inhibitory small molecule via an H-bonding interaction. A small minority of protein kinase domains has a Tyrosine residue in this position within the αC-β4 loop, and it is the only amino acid commonly seen here with H-bonding potential. These discoveries will aid design of inhibitors that discriminate among the JAK family and more widely among protein kinases.

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Organizational Affiliation: 

Department of Discovery Chemistry, Genentech, Inc, South San Francisco, California 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-receptor tyrosine-protein kinase TYK2	A	302	Homo sapiens	Mutation(s): 1  Gene Names: TYK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P29597 (Homo sapiens) Explore P29597  Go to UniProtKB:  P29597
PHAROS:  P29597

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TZ1	B [auth A]	N-{5-[(7-chloroquinolin-4-yl)sulfanyl]-1,3,4-thiadiazol-2-yl}thiophene-2-carboxamide C16 H9 Cl N4 O S3 KWDHWMGDHBBJIA-UHFFFAOYSA-N
DTT	C [auth A], D [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TZ1	PDBBind:  3NYX	Ki: 32 (nM) from 1 assay(s)
	Binding MOAD:  3NYX	Ki: 32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.318	α = 90
b = 70.436	β = 90
c = 86.488	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Eigenbrot, C., Ultsch, M.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance