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- PDB-6zc3: Small-molecule inhibitors of the PDZ domain of Dishevelled protei... -

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Basic information

Entry
Database: PDB / ID: 6zc3
TitleSmall-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling
ComponentsDishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
KeywordsPEPTIDE BINDING PROTEIN / PDZ / DVL / Inhibitors / Wnt / signalling
Function / homology
Function and homology information


: / frizzled binding / canonical Wnt signaling pathway / intracellular signal transduction / cytosol
Similarity search - Function
Dishevelled-3 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin ...Dishevelled-3 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
5-fluoranyl-2-(methylsulfonylamino)benzoic acid / Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRoske, Y. / Heinemann, U. / Oschkinat, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)806 Germany
CitationJournal: J.Magn.Reson. / Year: 2021
Title: Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling
Authors: 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. / ...Authors: 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.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
B: Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9285
Polymers20,3992
Non-polymers5293
Water3,693205
1
A: Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4953
Polymers10,2001
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4332
Polymers10,2001
Non-polymers2331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.276, 87.276, 57.844
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Dishevelled, dsh homolog 3 (Drosophila), isoform CRA_b


Mass: 10199.681 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp586M1622, DVL3, hCG_40299 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UG07
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-JOR / 5-fluoranyl-2-(methylsulfonylamino)benzoic acid


Mass: 233.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8FNO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.2 M ammonium sulphate, 0.1 M citric acid pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.67→34.84 Å / Num. obs: 29202 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rrim(I) all: 0.0055 / Net I/σ(I): 19.1
Reflection shellResolution: 1.67→1.71 Å / Num. unique obs: 2161 / Rrim(I) all: 0.0774

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F0A

2f0a


Resolution: 1.67→34.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.082 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1461 5 %RANDOM
Rwork0.1666 ---
obs0.1686 27741 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.36 Å2 / Biso mean: 30.414 Å2 / Biso min: 16.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.67→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1352 0 34 205 1591
Biso mean--31.06 47.9 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131431
X-RAY DIFFRACTIONr_bond_other_d00.0171367
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.6561946
X-RAY DIFFRACTIONr_angle_other_deg1.0621.5833154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5745192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23724.06364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22115246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.441157
X-RAY DIFFRACTIONr_chiral_restr0.0270.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021622
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02257
X-RAY DIFFRACTIONr_rigid_bond_restr0.51332798
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 109 -
Rwork0.22 2052 -
all-2161 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46210.209-0.22770.3721-0.03960.7933-0.0129-0.01560.00060.01420.00240.03220.0282-0.03550.01050.002400.00130.004-0.00010.0141-4.244829.8145-1.532
20.3313-0.21930.05830.25930.12590.3695-0.0042-0.01870.0251-0.00780.0105-0.0044-0.0099-0.0045-0.00630.00420.00060.00210.0031-0.00030.0178-26.074735.212911.9323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 336
2X-RAY DIFFRACTION2B244 - 336

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