6ZC8 | pdb_00006zc8

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

PDB DOI: https://doi.org/10.2210/pdb6ZC8/pdb

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

Deposited: 2020-06-10 Released: 2021-06-23
Deposition Author(s): Roske, Y., Heinemann, U., Oschkinat, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.285 (Depositor), 0.283 (DCC)
R-Value Work:
0.244 (Depositor), 0.243 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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

Macromolecule Content

Total Structure Weight: 21.4 kDa
Atom Count: 1,417
Modeled Residue Count: 176
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-3	A, B	95	Homo sapiens	Mutation(s): 0 Gene Names: DVL3, KIAA0208
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92997
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QEK (Subject of Investigation/LOI) Query on QEK Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-[[3-chloranyl-4-[(1~{H}-indazol-3-ylcarbonylamino)methyl]phenyl]sulfonylamino]-5-methyl-benzoic acid C₂₃ H₁₉ Cl N₄ O₅ S NSKPBPLCHQGVNU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.285 (Depositor), 0.283 (DCC)
R-Value Work: 0.244 (Depositor), 0.243 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.345	α = 90
b = 89.345	β = 90
c = 131.659	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

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

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.