5WE8

Crystal structure of WNK1 in complex with N-{(3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-yl}-2-(3-methoxyphenyl)-N-methylquinoline-4-carboxamide (compound 8)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Optimization of Allosteric With-No-Lysine (WNK) Kinase Inhibitors and Efficacy in Rodent Hypertension Models.

Yamada, K.Levell, J.Yoon, T.Kohls, D.Yowe, D.Rigel, D.F.Imase, H.Yuan, J.Yasoshima, K.DiPetrillo, K.Monovich, L.Xu, L.Zhu, M.Kato, M.Jain, M.Idamakanti, N.Taslimi, P.Kawanami, T.Argikar, U.A.Kunjathoor, V.Xie, X.Yagi, Y.I.Iwaki, Y.Robinson, Z.Park, H.M.

(2017) J Med Chem 60: 7099-7107

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00708
  • Primary Citation of Related Structures:  
    5WDY, 5WE8

  • PubMed Abstract: 

    The observed structure-activity relationship of three distinct ATP noncompetitive With-No-Lysine (WNK) kinase inhibitor series, together with a crystal structure of a previously disclosed allosteric inhibitor bound to WNK1, led to an overlay hypothesis defining core and side-chain relationships across the different series. This in turn enabled an efficient optimization through scaffold morphing, resulting in compounds with a good balance of selectivity, cellular potency, and pharmacokinetic profile, which were suitable for in vivo proof-of-concept studies. When dosed orally, the optimized compound reduced blood pressure in mice overexpressing human WNK1, and induced diuresis, natriuresis and kaliuresis in spontaneously hypertensive rats (SHR), confirming that this mechanism of inhibition of WNK kinase activity is effective at regulating cardiovascular homeostasis.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139-4133, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase WNK1
A, B
279Homo sapiensMutation(s): 4 
Gene Names: WNK1HSN2KDPKIAA0344PRKWNK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H4A3 (Homo sapiens)
Explore Q9H4A3 
Go to UniProtKB:  Q9H4A3
PHAROS:  Q9H4A3
GTEx:  ENSG00000060237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H4A3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
A7Y
Query on A7Y

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
N-{(3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-yl}-2-(3-methoxyphenyl)-N-methylquinoline-4-carboxamide
C29 H28 Cl N3 O2
UPCGOPZWVBKZPL-HSZRJFAPSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
A7Y BindingDB:  5WE8 IC50: 750 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.102α = 90
b = 105.235β = 117.28
c = 70.105γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations