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- PDB-7msb: Structure of EED bound to EEDi-4259 -

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Basic information

Entry
Database: PDB / ID: 7msb
TitleStructure of EED bound to EEDi-4259
ComponentsPolycomb protein EED
KeywordsGENE REGULATION/INHIBITOR / polycomb repressive complex 2 / GENE REGULATION-INHIBITOR complex
Function / homology
Function and homology information


ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / heterochromatin formation ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / heterochromatin formation / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / chromosome / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-ZNG / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPetrunak, E. / Stuckey, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA046592 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of EEDi-5273 as an Exceptionally Potent and Orally Efficacious EED Inhibitor Capable of Achieving Complete and Persistent Tumor Regression.
Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / Stuckey, J.A. / Zhou, Y. / ...Authors: Rej, R.K. / Wang, C. / Lu, J. / Wang, M. / Petrunak, E. / Zawacki, K.P. / McEachern, D. / Yang, C.Y. / Wang, L. / Li, R. / Chinnaswamy, K. / Wen, B. / Sun, D. / Stuckey, J.A. / Zhou, Y. / Chen, J. / Tang, G. / Wang, S.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8942
Polymers42,4121
Non-polymers4811
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.867, 85.024, 91.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 42412.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
#2: Chemical ChemComp-ZNG / (9aM,12aS)-12-{[(5-fluoro-1-benzofuran-4-yl)methyl]amino}-7-(trifluoromethyl)-4,5-dihydro-3H-2,4,11,12a-tetraazabenzo[4,5]cycloocta[1,2,3-cd]inden-3-one


Mass: 481.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H15F4N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2uL of protein + 2 uL of well (0.1 M Tris pH 8.5, 20% glycerol, 4.3 M Na Formate, 10 mM TCEP)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 36678 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.61 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.037 / Rrim(I) all: 0.101 / Χ2: 0.947 / Net I/σ(I): 7.3 / Num. measured all: 269118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.937.30.66117990.8550.2620.7110.843100
1.93-1.977.40.58317860.8740.230.6270.843100
1.97-2.017.40.48618120.9170.1910.5230.882100
2.01-2.057.40.4318010.9280.1690.4620.889100
2.05-2.097.40.3718360.9420.1450.3980.935100
2.09-2.147.40.31918050.9620.1250.3430.922100
2.14-2.197.40.28617970.9650.1120.3080.92100
2.19-2.257.40.25318110.9710.0990.2720.931100
2.25-2.327.40.24618170.9750.0960.2640.973100
2.32-2.397.50.21118010.9820.0820.2261.011100
2.39-2.487.40.19918280.9790.0780.2141.074100
2.48-2.587.40.16418230.9860.0640.1761.112100
2.58-2.77.40.14218150.9890.0560.1521.083100
2.7-2.847.40.11118410.9930.0440.121.042100
2.84-3.027.40.08318410.9960.0330.0890.95100
3.02-3.257.40.06218390.9970.0250.0671.014100
3.25-3.587.20.05218650.9980.0210.0561.236100
3.58-4.097.20.0418560.9980.0160.0431.017100
4.09-5.1670.02719050.9990.0110.0290.665100
5.16-506.70.02720000.9990.0110.0290.58199.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house structure

Resolution: 1.9→18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1799 4.93 %RANDOM
Rwork0.16 ---
obs0.162 36515 99.7 %-
Displacement parametersBiso max: 108.43 Å2 / Biso mean: 23.28 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.9715 Å20 Å20 Å2
2--0.1026 Å20 Å2
3----1.0742 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.9→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 35 417 3319
Biso mean--19.09 40.86 -
Num. residues----359
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1386SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes551HARMONIC5
X-RAY DIFFRACTIONt_it3013HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion387SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3753SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3013HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4105HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion4.2
X-RAY DIFFRACTIONt_other_torsion2.79
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2012 29 3.97 %
Rwork0.1978 702 -
all0.1979 731 -
obs--88.57 %

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