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- PDB-8p29: TEAD2 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 8p29
TitleTEAD2 in complex with an inhibitor
ComponentsTranscriptional enhancer factor TEF-4
KeywordsSIGNALING PROTEIN / 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
MYRISTIC ACID / Chem-WJC / Transcriptional enhancer factor TEF-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsGuichou, J.F. / Gelin, M. / Allemand, F.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Development of LM-41 and AF-2112, two flufenamic acid-derived TEAD inhibitors obtained through the replacement of the trifluoromethyl group by aryl rings.
Authors: Fnaiche, A. / Melin, L. / Suarez, N.G. / Paquin, A. / Vu, V. / Li, F. / Allali-Hassani, A. / Bolotokova, A. / Allemand, F. / Gelin, M. / Cotelle, P. / Woo, S. / LaPlante, S.R. / Barsyte- ...Authors: Fnaiche, A. / Melin, L. / Suarez, N.G. / Paquin, A. / Vu, V. / Li, F. / Allali-Hassani, A. / Bolotokova, A. / Allemand, F. / Gelin, M. / Cotelle, P. / Woo, S. / LaPlante, S.R. / Barsyte-Lovejoy, D. / Santhakumar, V. / Vedadi, M. / Guichou, J.F. / Annabi, B. / Gagnon, A.
History
DepositionMay 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)55,6325
Polymers54,9782
Non-polymers6543
Water1,00956
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)27,9153
Polymers27,4891
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.842, 61.652, 80.018
Angle α, β, γ (deg.)90.00, 117.51, 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 / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-WJC / 5-methyl-2-[(3-phenylmethoxyphenyl)amino]benzoic acid


Mass: 333.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.42 Å3/Da / Density % sol: 49.16 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.06→57.72 Å / Num. obs: 58253 / % possible obs: 98.76 % / Redundancy: 1.8 % / CC1/2: 0.998 / Net I/σ(I): 9.63
Reflection shellResolution: 2.06→2.13 Å / Num. unique obs: 3205 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→57.72 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2953 5.07 %
Rwork0.1954 --
obs0.1978 58253 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→57.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 47 56 3433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084
X-RAY DIFFRACTIONf_angle_d0.9314
X-RAY DIFFRACTIONf_dihedral_angle_d9.138482
X-RAY DIFFRACTIONf_chiral_restr0.056506
X-RAY DIFFRACTIONf_plane_restr0.01608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.35261460.31112571X-RAY DIFFRACTION89
2.09-2.130.30261140.29542622X-RAY DIFFRACTION89
2.13-2.160.27651220.25932614X-RAY DIFFRACTION91
2.16-2.210.30731370.26382698X-RAY DIFFRACTION91
2.21-2.250.3081380.24832660X-RAY DIFFRACTION92
2.25-2.30.27831490.23592633X-RAY DIFFRACTION91
2.3-2.350.26021180.22672767X-RAY DIFFRACTION93
2.35-2.410.28011610.22712646X-RAY DIFFRACTION93
2.41-2.480.29241500.22622673X-RAY DIFFRACTION93
2.48-2.550.28631200.23532727X-RAY DIFFRACTION93
2.55-2.630.32931500.25132709X-RAY DIFFRACTION93
2.63-2.730.25021160.25282654X-RAY DIFFRACTION91
2.73-2.840.32971310.23762716X-RAY DIFFRACTION92
2.84-2.970.27161500.23872610X-RAY DIFFRACTION91
2.97-3.120.2621430.24622573X-RAY DIFFRACTION89
3.12-3.320.24651480.20512596X-RAY DIFFRACTION91
3.32-3.570.26431650.18642603X-RAY DIFFRACTION90
3.57-3.930.21931370.16762615X-RAY DIFFRACTION90
3.93-4.50.19461530.14712599X-RAY DIFFRACTION90
4.5-5.670.19331380.14952572X-RAY DIFFRACTION88
5.67-57.720.21311670.17672442X-RAY DIFFRACTION86
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)
17.95751.10582.93222.5580.79036.01090.0103-0.0071-0.2411-0.0480.0173-0.26440.36350.15270.01090.45430.02980.06580.27680.02480.2421-29.828-12.42221.677
23.53350.65041.65241.71620.73055.6005-0.0252-0.261-0.0688-0.049-0.03380.00780.1506-0.42050.04760.4290.02550.07480.28250.03810.2792-33.356-9.76819.21
37.1575-0.0815-1.73125.174-0.65126.4602-0.05220.43030.0877-0.26730.28750.3943-0.5703-0.3473-0.25970.54870.07840.11340.41970.01980.3313-42.22519.43320.178
44.14560.2048-4.31441.3767-0.65827.98590.1412-0.58960.2120.10560.10280.0219-0.32190.4897-0.20770.55470.07170.07950.36880.00720.3668-36.85517.39721.051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 220:293 )B220 - 293
2X-RAY DIFFRACTION2( CHAIN B AND RESID 294:456 )B294 - 456
3X-RAY DIFFRACTION3( CHAIN A AND RESID 222:293 )A222 - 293
4X-RAY DIFFRACTION4( CHAIN A AND RESID 294:446 )A294 - 446

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