JAK1 complexed with compound 28

Experimental Data Snapshot

  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The Discovery of 3-((4-Chloro-3-methoxyphenyl)amino)-1-((3R,4S)-4-cyanotetrahydro-2H-pyran-3-yl)-1H-pyrazole-4-carboxamide, a Highly Ligand Efficient and Efficacious Janus Kinase 1 Selective Inhibitor with Favorable Pharmacokinetic Properties.

Siu, T.Brubaker, J.Fuller, P.Torres, L.Zeng, H.Close, J.Mampreian, D.M.Shi, F.Liu, D.Fradera, X.Johnson, K.Bays, N.Kadic, E.He, F.Goldenblatt, P.Shaffer, L.Patel, S.B.Lesburg, C.A.Alpert, C.Dorosh, L.Deshmukh, S.V.Yu, H.Klappenbach, J.Elwood, F.Dinsmore, C.J.Fernandez, R.Moy, L.Young, J.R.

(2017) J Med Chem 60: 9676-9690

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b01135
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The discovery of a potent selective low dose Janus kinase 1 (JAK1) inhibitor suitable for clinical evaluation is described. As part of an overall goal to minimize dose, we pursued a medicinal chemistry strategy focused on optimization of key parameters that influence dose size, including lowering human Cl int and increasing intrinsic potency, bioavailability, and solubility. To impact these multiple parameters simultaneously, we used lipophilic ligand efficiency as a key metric to track changes in the physicochemical properties of our analogs, which led to improvements in overall compound quality. In parallel, structural information guided advancements in JAK1 selectivity by informing on new vector space, which enabled the discovery of a unique key amino acid difference between JAK1 (Glu966) and JAK2 (Asp939). This difference was exploited to consistently produce analogs with the best balance of JAK1 selectivity, efficacy, and projected human dose, ultimately culminating in the discovery of compound 28.

  • Organizational Affiliation

    Department of Medicinal Chemistry, ‡Department of Discovery Process Chemistry, §Department of Modeling & Informatics, ∥Department of In Vitro Pharmacology, ⊥Department of Structural Chemistry, #Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, ∇Department of Discovery Pharmaceutical Sciences, ○Department of Molecular Biomarkers, ¶Department of In Vivo Pharmacology, $Department of Respiratory and Immunology, Merck & Co., Inc. , 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
Gene Names: JAK1JAK1AJAK1B
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
PHAROS:  P23458
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B7V (Subject of Investigation/LOI)
Query on B7V

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C17 H18 Cl N5 O3
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PTR
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
B7V BindingDB:  5WO4 IC50: min: 0.1, max: 13 (nM) from 3 assay(s)
Binding MOAD:  5WO4 IC50: 0.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.57α = 90
b = 173.36β = 93.94
c = 44.65γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
AutoPROCdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2017-12-27
    Changes: Database references