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- PDB-8pux: TEAD2 with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 8pux
TitleTEAD2 with a covalent inhibitor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsSIGNALING PROTEIN / TEAD2 / Inhibitor / Covalent
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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / 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-B3F / MYRISTIC ACID / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGuichou, J.F. / Gelin, M. / Allemand, F.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Development of HC-258, a Covalent Acrylamide TEAD Inhibitor That Reduces Gene Expression and Cell Migration.
Authors: Fnaiche, A. / Chan, H.C. / Paquin, A. / Gonzalez Suarez, N. / Vu, V. / Li, F. / Allali-Hassani, A. / Cao, M.A. / Szewczyk, M.M. / Bolotokova, A. / Allemand, F. / Gelin, M. / Barsyte-Lovejoy, ...Authors: Fnaiche, A. / Chan, H.C. / Paquin, A. / Gonzalez Suarez, N. / Vu, V. / Li, F. / Allali-Hassani, A. / Cao, M.A. / Szewczyk, M.M. / Bolotokova, A. / Allemand, F. / Gelin, M. / Barsyte-Lovejoy, D. / Santhakumar, V. / Vedadi, M. / Guichou, J.F. / Annabi, B. / Gagnon, A.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
B: Transcriptional enhancer factor TEF-4
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5334
Polymers54,9782
Non-polymers5552
Water72140
1
B: 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
A: Transcriptional enhancer factor TEF-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8162
Polymers27,4891
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.306, 61.613, 79.704
Angle α, β, γ (deg.)90.00, 117.55, 90.00
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.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-B3F / ~{N}-[2-[(3-pentoxyphenyl)amino]phenyl]propanamide


Mass: 326.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.97 %
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: 0.9697 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9697 Å / Relative weight: 1
ReflectionResolution: 2.05→54.28 Å / Num. obs: 33152 / % possible obs: 99.73 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 11.63
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 3290 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→54.28 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.661 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26051 1613 5 %RANDOM
Rwork0.21956 ---
obs0.22152 30627 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.1 Å2
2--0.19 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→54.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 38 40 3400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133465
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173214
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6434685
X-RAY DIFFRACTIONr_angle_other_deg1.2491.5837378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8555409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.90621.25200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31615565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2581527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8146.1661639
X-RAY DIFFRACTIONr_mcbond_other4.8146.1651638
X-RAY DIFFRACTIONr_mcangle_it7.0849.2162038
X-RAY DIFFRACTIONr_mcangle_other7.0829.2172039
X-RAY DIFFRACTIONr_scbond_it5.0956.6121826
X-RAY DIFFRACTIONr_scbond_other5.0936.6121827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5599.7412645
X-RAY DIFFRACTIONr_long_range_B_refined11.441113368
X-RAY DIFFRACTIONr_long_range_B_other11.441113369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å
RfactorNum. reflection% reflection
Rfree0.418 122 -
Rwork0.417 2223 -
obs--97.1 %

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