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- PDB-9ixt: Crystal structure of TEAD3 YAP binding domain with compound 2 -

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Basic information

Entry
Database: PDB / ID: 9ixt
TitleCrystal structure of TEAD3 YAP binding domain with compound 2
ComponentsTranscriptional enhancer factor TEF-5
KeywordsTRANSCRIPTION / transcription factor / TEAD3
Function / homology
Function and homology information


asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...asymmetric neuroblast division / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / embryonic organ development / female pregnancy / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Transcriptional enhancer factor TEF-5 (TEAD3) / 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
: / Transcriptional enhancer factor TEF-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoo, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2025
Title: Structure-based optimization of TEAD inhibitors: Exploring a novel subpocket near Glu347 for the treatment of NF2-mutant cancer.
Authors: Kim, J.K. / Kim, J. / Kim, H. / Jin, H. / Yoo, Y. / Fei, X. / Maeng, H.J. / Seo, S.Y. / Han, G. / No, K.T.
History
DepositionJul 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-5
B: Transcriptional enhancer factor TEF-5
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8036
Polymers76,3593
Non-polymers1,4453
Water1,946108
1
A: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9342
Polymers25,4531
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9342
Polymers25,4531
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional enhancer factor TEF-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9342
Polymers25,4531
Non-polymers4821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.180, 102.610, 148.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transcriptional enhancer factor TEF-5 / DTEF-1 / TEA domain family member 3 / TEAD-3


Mass: 25452.918 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N terminal Glycine is protease cleavage site / Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD3, TEAD5, TEF5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99594
#2: Chemical ChemComp-A1L3M / ~{N}-[(1~{S})-4-azanyl-4-oxidanylidene-1-phenyl-butyl]-5-[4-(trifluoromethyl)phenyl]-3,4-dihydro-1~{H}-isoquinoline-2-carboxamide


Mass: 481.509 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H26F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 0.2M Ammonium acetate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→28.96 Å / Num. obs: 25187 / % possible obs: 99.64 % / Redundancy: 12.7 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2319 / Net I/σ(I): 13.22
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.7634 / Mean I/σ(I) obs: 4.22 / Num. unique obs: 2466 / CC1/2: 0.896

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.96 Å / SU ML: 0.2933 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 2000 7.94 %
Rwork0.2058 23183 -
obs0.2093 25183 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 105 108 5472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00965612
X-RAY DIFFRACTIONf_angle_d1.29367591
X-RAY DIFFRACTIONf_chiral_restr0.071795
X-RAY DIFFRACTIONf_plane_restr0.0092960
X-RAY DIFFRACTIONf_dihedral_angle_d17.17692050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.32681410.26071642X-RAY DIFFRACTION99.72
2.56-2.630.35681390.261599X-RAY DIFFRACTION100
2.63-2.710.33481420.26941655X-RAY DIFFRACTION100
2.71-2.80.30761380.23881593X-RAY DIFFRACTION99.83
2.8-2.90.32251440.22471665X-RAY DIFFRACTION100
2.9-3.010.27911400.23351620X-RAY DIFFRACTION100
3.01-3.150.26271400.23891636X-RAY DIFFRACTION99.55
3.15-3.310.27951440.22071668X-RAY DIFFRACTION99.89
3.31-3.520.24351420.20791643X-RAY DIFFRACTION99.89
3.52-3.790.23621420.19341655X-RAY DIFFRACTION100
3.79-4.170.23941430.18411655X-RAY DIFFRACTION99.28
4.17-4.780.19151440.16581671X-RAY DIFFRACTION100
4.78-60.23251470.18981709X-RAY DIFFRACTION99.68
6.01-28.960.19391540.19411772X-RAY DIFFRACTION98.62

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