6ZBZ

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QE5Click on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling

Roske, Y.Heinemann, U.Oschkinat, H.Kamdem, N.Kovalskyy, D.Platonov, M.O.Balinskyi, O.M.Kreuchwig, A.Saupe, J.Fang, L.Diehl, A.Schmieder, P.Krause, G.Rademann, J.Birchmeier, W.

(2021) J Magn Reson (1969 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
A, B, C, D
95Homo sapiensMutation(s): 0 
Gene Names: DKFZp586M1622DVL3hCG_40299
UniProt & NIH Common Fund Data Resources
Find proteins for Q92997 (Homo sapiens)
Explore Q92997 
Go to UniProtKB:  Q92997
PHAROS:  Q92997
GTEx:  ENSG00000161202 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92997
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QE5 (Subject of Investigation/LOI)
Query on QE5

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
H [auth C],
K [auth D]
2-[(3,4-dimethylphenyl)sulfonylamino]-5-fluoranyl-benzoic acid
C15 H14 F N O4 S
FDKADOFRLAUJSY-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth B],
I [auth C],
J [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.837α = 90
b = 70.059β = 90
c = 87.182γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QE5Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany806

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description