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- PDB-6s64: Crystal structure of hTEAD2 in complex with a trisubstituted pyra... -

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Basic information

Entry
Database: PDB / ID: 6s64
TitleCrystal structure of hTEAD2 in complex with a trisubstituted pyrazole inhibitor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsTRANSCRIPTION / TEAD2 / Inhibitor
Function / homology
Function and homology information


TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis ...TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / disordered domain specific binding / sequence-specific double-stranded DNA binding / protein-containing complex assembly / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain
Similarity search - Domain/homology
Chem-KXE / MYRISTIC ACID / PALMITIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.22 Å
AuthorsSturbaut, M. / Allemand, F. / Guichou, J.F.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Discovery of a cryptic site at the interface 2 of TEAD - Towards a new family of YAP/TAZ-TEAD inhibitors.
Authors: Sturbaut, M. / Bailly, F. / Coevoet, M. / Sileo, P. / Pugniere, M. / Liberelle, M. / Magnez, R. / Thuru, X. / Chartier-Harlin, M.C. / Melnyk, P. / Gelin, M. / Allemand, F. / Guichou, J.F. / Cotelle, P.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: Transcriptional enhancer factor TEF-4
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8815
Polymers54,9782
Non-polymers9033
Water41423
1
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7172
Polymers27,4891
Non-polymers2281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1643
Polymers27,4891
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.690, 61.655, 80.240
Angle α, β, γ (deg.)90.000, 117.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcriptional enhancer factor TEF-4 / TEA domain family member 2 / TEAD-2


Mass: 27489.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15562
#2: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-KXE / 3-[3-(3,4-dichlorophenyl)-4-[(phenylmethyl)carbamoyl]pyrazol-1-yl]propanoic acid


Mass: 418.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17Cl2N3O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.22→71.26 Å / Num. obs: 26130 / % possible obs: 96.4 % / Redundancy: 1.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Net I/σ(I): 13.1
Reflection shellResolution: 2.22→2.3 Å / Rmerge(I) obs: 0.372 / Num. unique obs: 2603 / CC1/2: 0.886 / % possible all: 96.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→71.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.227 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1296 5 %RANDOM
Rwork0.2033 ---
obs0.2061 24733 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.55 Å2 / Biso mean: 67.334 Å2 / Biso min: 36 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.05 Å2
2--0.13 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.22→71.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 61 23 3411
Biso mean--78.8 60.18 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193487
X-RAY DIFFRACTIONr_bond_other_d0.0060.023317
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9464697
X-RAY DIFFRACTIONr_angle_other_deg0.96937605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5485404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52922.865178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11715590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8491531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
LS refinement shellResolution: 2.222→2.279 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 100 -
Rwork0.45 1844 -
all-1944 -
obs--99.23 %

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