5WDY

Crystal structure of WNK1 in complex with 1-cyclohexyl-N-({6-fluoro-1-[2-(3-methoxyphenyl)pyridin-4-yl]-1H-indol-3-yl}methyl)methanamine (compound 6)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.7b00708
  • Primary Citation of Related Structures:  
    5WE8, 5WDY

  • 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 ...

    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, Novartis Pharma K.K. , Tsukuba, Ibaraki 300-2611, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase WNK1 AB279Homo sapiensMutation(s): 4 
Gene Names: WNK1HSN2KDPKIAA0344PRKWNK1
EC: 2.7.11.1
Find proteins for Q9H4A3 (Homo sapiens)
Explore Q9H4A3 
Go to UniProtKB:  Q9H4A3
NIH Common Fund Data Resources
PHAROS:  Q9H4A3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
A6S
Query on A6S

Download Ideal Coordinates CCD File 
A, B
1-cyclohexyl-N-({6-fluoro-1-[2-(3-methoxyphenyl)pyridin-4-yl]-1H-indol-3-yl}methyl)methanamine
C28 H30 F N3 O
MDKNOMUATKMYAA-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.334α = 67.13
b = 62.267β = 77.42
c = 70.268γ = 74.74
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-07-06 
  • Released Date: 2017-08-16 
  • Deposition Author(s): Xie, X., Kohls, D.

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