6ZBZ | pdb_00006zbz

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

• PDB DOI: https://doi.org/10.2210/pdb6ZBZ/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-09 Released: 2021-06-23 
• Deposition Author(s): Roske, Y., Heinemann, U., Oschkinat, H.
• Funding Organization(s): German Research Foundation (DFG)

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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), 0.182 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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 

• DOI: https://doi.org/10.5194/mr-2-355-2021

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.28 kDa 
• Atom Count: 3,228 
• Modeled Residue Count: 359 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b	A, B, C, D	95	Homo sapiens	Mutation(s): 0  Gene Names: DKFZp586M1622, DVL3, hCG_40299
UniProt & NIH Common Fund Data Resources
Find proteins for Q92997 (Homo sapiens) Explore Q92997  Go to UniProtKB:  Q92997
PHAROS:  Q92997 GTEx:  ENSG00000161202

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QE5 (Subject of Investigation/LOI)	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	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), 0.182 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.837	α = 90
b = 70.059	β = 90
c = 87.182	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Roske, Y., Heinemann, U., Oschkinat, H.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	806

Revision History  

• 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