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- PDB-6tfb: Carbamazepine binds Frizzled8 -

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Basic information

Entry
Database: PDB / ID: 6tfb
TitleCarbamazepine binds Frizzled8
ComponentsFrizzled-8
KeywordsONCOPROTEIN / Wnt receptor Frizzled8 carbamazepine
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / PDZ domain binding / G protein-coupled receptor activity ...Wnt-Frizzled-LRP5/6 complex / Regulation of FZD by ubiquitination / Asymmetric localization of PCP proteins / Wnt receptor activity / non-canonical Wnt signaling pathway / Wnt-protein binding / neuronal dense core vesicle / canonical Wnt signaling pathway / PDZ domain binding / G protein-coupled receptor activity / Wnt signaling pathway / cell-cell signaling / T cell differentiation in thymus / angiogenesis / positive regulation of protein phosphorylation / signaling receptor binding / ubiquitin protein ligase binding / Golgi apparatus / extracellular region / plasma membrane
Similarity search - Function
Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. ...Frizzled 8, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2.
Similarity search - Domain/homology
benzo[b][1]benzazepine-11-carboxamide / Frizzled-8
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Antiepileptic Drug Carbamazepine Binds to a Novel Pocket on the Wnt Receptor Frizzled-8.
Authors: Zhao, Y. / Ren, J. / Hillier, J. / Lu, W. / Jones, E.Y.
History
DepositionNov 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Frizzled-8
B: Frizzled-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3797
Polymers31,6302
Non-polymers7495
Water1,36976
1
A: Frizzled-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2364
Polymers15,8151
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Frizzled-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1433
Polymers15,8151
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.002, 68.143, 73.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Frizzled-8 / mFz8


Mass: 15815.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fzd8 / Cell line (production host): HEK293S GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q61091
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-N6W / benzo[b][1]benzazepine-11-carboxamide


Mass: 236.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, pH 5 1 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.68→52 Å / Num. obs: 30318 / % possible obs: 99.2 % / Redundancy: 11.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.4
Reflection shellResolution: 1.68→1.71 Å / Mean I/σ(I) obs: 8.5 / Num. unique obs: 1412 / CC1/2: 0.84

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Processing

Software
NameVersionClassification
PHENIXv1.0refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IJY

1ijy


Resolution: 1.68→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2654 --
Rwork0.2005 --
obs-45445 99.2 %
Displacement parametersBiso max: 66.46 Å2 / Biso mean: 28 Å2 / Biso min: 2.54 Å2
Refinement stepCycle: LAST / Resolution: 1.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 54 76 2179

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