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- PDB-6s60: Crystal structure of hTEAD2 in complex with a trisubstituted pyra... -

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Basic information

Entry
Database: PDB / ID: 6s60
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 / Formation of axial mesoderm / regulation of stem cell differentiation / 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 / Formation of axial mesoderm / regulation of stem cell differentiation / embryonic heart tube morphogenesis / embryonic organ development / vasculogenesis / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / sequence-specific double-stranded DNA binding / disordered domain specific 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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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-KX8 / MYRISTIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)55,8675
Polymers54,9782
Non-polymers8893
Water1,856103
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)28,1503
Polymers27,4891
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.780, 61.676, 79.999
Angle α, β, γ (deg.)90.000, 117.660, 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


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-KX8 / 4-[3-(3,4-dichlorophenyl)-4-[(phenylmethyl)carbamoyl]pyrazol-1-yl]butanoic acid


Mass: 432.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19Cl2N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.99 %
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→70.86 Å / Num. obs: 35914 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.027 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.332 / Num. unique obs: 3572 / CC1/2: 0.879 / % possible all: 99.1

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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
Starting model: 5DQE

5dqe


Resolution: 2→70.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.628 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.151
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1814 5.1 %RANDOM
Rwork0.1909 ---
obs0.1928 33965 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.14 Å2 / Biso mean: 52.87 Å2 / Biso min: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20.71 Å2
2---0.01 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: final / Resolution: 2→70.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 59 103 3559
Biso mean--62.01 53.38 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193566
X-RAY DIFFRACTIONr_bond_other_d0.0020.023383
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.9514807
X-RAY DIFFRACTIONr_angle_other_deg1.01537767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8155419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31322.768177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25615600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5091532
X-RAY DIFFRACTIONr_chiral_restr0.1120.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 132 -
Rwork0.381 2496 -
all-2628 -
obs--98.57 %

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