5WO4

JAK1 complexed with compound 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acs.jmedchem.7b01135

  • 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 paramete ...

    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 Clint 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
Gene Names: JAK1 (JAK1A, JAK1B)
EC: 2.7.10.2
Find proteins for P23458 (Homo sapiens)
Go to Gene View: JAK1
Go to UniProtKB:  P23458
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B7V
Query on B7V

Download SDF File 
Download CCD File 
A, B
3-[(4-chloro-3-methoxyphenyl)amino]-1-[(3R,4S)-4-cyanooxan-3-yl]-1H-pyrazole-4-carboxamide
C17 H18 Cl N5 O3
MFWQXZZXOUIDTN-YGRLFVJLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.570α = 90.00
b = 173.360β = 93.94
c = 44.650γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata scaling
autoBUSTERphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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