5TF9

Crystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery and Characterization of Allosteric WNK Kinase Inhibitors.

Yamada, K.Zhang, J.H.Xie, X.Reinhardt, J.Xie, A.Q.LaSala, D.Kohls, D.Yowe, D.Burdick, D.Yoshisue, H.Wakai, H.Schmidt, I.Gunawan, J.Yasoshima, K.Yue, Q.K.Kato, M.Mogi, M.Idamakanti, N.Kreder, N.Drueckes, P.Pandey, P.Kawanami, T.Huang, W.Yagi, Y.I.Deng, Z.Park, H.M.

(2016) ACS Chem Biol 11: 3338-3346

  • DOI: 10.1021/acschembio.6b00511
  • Primary Citation of Related Structures:  
    5TF9

  • PubMed Abstract: 
  • Protein kinases are known for their highly conserved adenosine triphosphate (ATP)-binding site, rendering the discovery of selective inhibitors a major challenge. In theory, allosteric inhibitors can achieve high selectivity by targeting less conserved regions of the kinases, often with an added benefit of retaining efficacy under high physiological ATP concentration ...

    Protein kinases are known for their highly conserved adenosine triphosphate (ATP)-binding site, rendering the discovery of selective inhibitors a major challenge. In theory, allosteric inhibitors can achieve high selectivity by targeting less conserved regions of the kinases, often with an added benefit of retaining efficacy under high physiological ATP concentration. Although often overlooked in favor of ATP-site directed approaches, performing a screen at high ATP concentration or stringent hit triaging with high ATP concentration offers conceptually simple methods of identifying inhibitors that bind outside the ATP pocket. Here, we applied the latter approach to the With-No-Lysine (K) (WNK) kinases to discover lead molecules for a next-generation antihypertensive that requires a stringent safety profile. This strategy yielded several ATP noncompetitive WNK1-4 kinase inhibitors, the optimization of which enabled cocrystallization with WNK1, revealing an allosteric binding mode consistent with the observed exquisite specificity for WNK1-4 kinases. The optimized compound inhibited rubidium uptake by sodium chloride cotransporter 1 (NKCC1) in HT29 cells, consistent with the reported physiology of WNK kinases in renal electrolyte handling.


    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): 0 
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 4 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
7AV
Query on 7AV

Download Ideal Coordinates CCD File 
A, B
{2-[(4-chlorophenyl)methoxy]phenyl}{5-[2-(methylamino)-1,3-thiazol-4-yl]-2,3-dihydro-1H-indol-1-yl}methanone
C26 H22 Cl N3 O2 S
GOAZOFMNXDONAU-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7AVIC50:  150   nM  BindingDB
7AVIC50:  377   nM  BindingDB
7AVIC50:  50   nM  BindingDB
7AVIC50:  64   nM  BindingDB
7AVIC50:  420   nM  BindingDB
7AVIC50:  180   nM  BindingDB
7AVKd:  4400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.065α = 90
b = 104.482β = 116.5
c = 69.604γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-09-24 
  • Released Date: 2016-10-19 
  • Deposition Author(s): Xie, X., Gunawan, J.

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references