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


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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, 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): 0 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
7AV
Query on 7AV

Download Ideal Coordinates CCD File 
C [auth A],
G [auth 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
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7AV Binding MOAD:  5TF9 Kd: 4400 (nM) from 1 assay(s)
BindingDB:  5TF9 IC50: min: 50, max: 420 (nM) from 6 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description