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- PDB-7qk4: EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683) -

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Basic information

Entry
Database: PDB / ID: 7qk4
TitleEED in complex with PRC2 allosteric inhibitor compound 22 (MAK683)
Components
  • Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
KeywordsTRANSFERASE / Inhibitor / Complex
Function / homology
Function and homology information


regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / primary miRNA binding ...regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / positive regulation of cell cycle G1/S phase transition / : / chromatin silencing complex / ESC/E(Z) complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / G1 to G0 transition / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of gene expression, epigenetic / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / nucleosome binding / enzyme activator activity / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / keratinocyte differentiation / protein localization to chromatin / B cell differentiation / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / liver regeneration / stem cell differentiation / promoter-specific chromatin binding / hippocampus development / positive regulation of MAP kinase activity / protein modification process / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / G1/S transition of mitotic cell cycle / chromatin DNA binding / PKMTs methylate histone lysines / positive regulation of GTPase activity / cellular response to hydrogen peroxide / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / rhythmic process / response to estradiol / chromosome / chromatin organization / Oxidative Stress Induced Senescence / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / synapse / chromatin binding / chromatin / positive regulation of cell population proliferation / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
EZH2, SET domain / : / Ezh2, MCSS domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Tesmin/TSO1-like CXC domain ...EZH2, SET domain / : / Ezh2, MCSS domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / CXC domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SET domain / SET domain profile. / SET domain / SANT/Myb domain / 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-EJR / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 Å
AuthorsZhao, K. / Zhao, M. / Luo, X. / Zhang, H. / Scheufler, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of the Clinical Candidate MAK683: An EED-Directed, Allosteric, and Selective PRC2 Inhibitor for the Treatment of Advanced Malignancies.
Authors: Huang, Y. / Sendzik, M. / Zhang, J. / Gao, Z. / Sun, Y. / Wang, L. / Gu, J. / Zhao, K. / Yu, Z. / Zhang, L. / Zhang, Q. / Blanz, J. / Chen, Z. / Dubost, V. / Fang, D. / Feng, L. / Fu, X. / ...Authors: Huang, Y. / Sendzik, M. / Zhang, J. / Gao, Z. / Sun, Y. / Wang, L. / Gu, J. / Zhao, K. / Yu, Z. / Zhang, L. / Zhang, Q. / Blanz, J. / Chen, Z. / Dubost, V. / Fang, D. / Feng, L. / Fu, X. / Kiffe, M. / Li, L. / Luo, F. / Luo, X. / Mi, Y. / Mistry, P. / Pearson, D. / Piaia, A. / Scheufler, C. / Terranova, R. / Weiss, A. / Zeng, J. / Zhang, H. / Zhang, J. / Zhao, M. / Dillon, M.P. / Jeay, S. / Qi, W. / Moggs, J. / Pissot-Soldermann, C. / Li, E. / Atadja, P. / Lingel, A. / Oyang, C.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: 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 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: Histone-lysine N-methyltransferase EZH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3326
Polymers45,8492
Non-polymers4834
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.456, 91.202, 179.016
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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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: 42227.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal glycine left after TEV cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
#2: Protein/peptide Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 3622.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q15910, [histone H3]-lysine27 N-trimethyltransferase
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EJR / N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine


Mass: 376.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17FN6O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.0, 0.2 M MgCl2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.602→19.96 Å / Num. obs: 43547 / % possible obs: 84.5 % / Redundancy: 6.69 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.143 / Rmerge(I) obs: 0.0583 / Rpim(I) all: 0.024 / Rrim(I) all: 0.0632 / AbsDiff over sigma anomalous: 0.678 / Baniso tensor eigenvalue 1: 15.2 Å2 / Baniso tensor eigenvalue 2: 29.6 Å2 / Baniso tensor eigenvalue 3: 20.6 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.522 Å / Aniso diffraction limit 2: 1.753 Å / Aniso diffraction limit 3: 1.622 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 17.13 / Num. measured all: 291362 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 84 / % possible ellipsoidal: 84.5 / % possible ellipsoidal anomalous: 84 / % possible spherical: 79.6 / % possible spherical anomalous: 79.1 / Redundancy anomalous: 3.51 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.693-19.966.320.037437.641375413754217621760.998-0.0840.0160.04080.6393.694.493.694.493.63.5894.4
3.724-4.6936.570.040438.271430814308217921790.998-0.1650.01690.04390.67496.997.596.997.596.93.5697.5
3.231-3.7246.770.043636.31473114731217721770.998-0.1870.01790.04720.69491.992.191.992.191.93.6192.1
2.944-3.2316.960.046132.961514815148217721770.998-0.1840.01870.04980.70799.910099.910099.93.68100
2.735-2.9447.060.051629.571536915369217721770.998-0.1440.02080.05570.73299.999.999.999.999.93.7199.9
2.559-2.7357.130.061425.871553115531217821780.998-0.1660.02460.06620.70788.488.588.488.588.43.7488.5
2.434-2.5597.180.068223.051563315633217721770.997-0.1660.02730.07350.721001001001001003.76100
2.33-2.4347.220.076420.891571915719217721770.997-0.1450.03050.08240.71510099.910099.91003.7799.9
2.209-2.337.20.08718.61567715677217821780.996-0.150.03480.09380.70270.470.770.470.770.43.7670.7
2.137-2.2097.270.099316.661583015830217821780.996-0.1470.03950.1070.6861001001001001003.78100
2.018-2.1377.210.119813.971568415684217621760.995-0.0590.04780.12920.71250.550.750.550.750.53.7650.7
1.967-2.0187.320.158511.141593115931217721770.992-0.0320.06280.17070.6981001001001001003.79100
1.871-1.9676.980.21968.191521915219217921790.988-0.0250.08830.23710.68944.946.244.946.244.93.746.2
1.833-1.8717.320.30486.581592315923217521750.979-0.030.12020.3280.6681001001001001003.78100
1.797-1.8337.310.37555.511593915939218021800.964-0.0080.14790.40390.65999.699.599.699.599.63.7899.5
1.763-1.7977.140.42814.881553615536217621760.9610.0080.1710.46160.64794.194.294.194.294.13.6994.2
1.728-1.7636.050.44934.081317113171217821780.945-0.0240.19520.49110.63489.58989.58686.93.189
1.69-1.7285.470.48843.411190811908217621760.918-0.0230.22360.53890.62786.586.386.574.574.92.886.3
1.649-1.695.020.53192.91094210942217921790.885-0.0060.25790.59370.63885.185.585.161.361.52.5785.5
1.602-1.6494.320.61292.1994099409217721770.833-0.0360.3230.6970.62172.974.972.948.947.12.2774.9

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Processing

Software
NameVersionClassification
autoPROC1.1.7 20210420data processing
autoPROCJan 31, 2020data processing
STARANISO0.7.7data scaling
autoPROC2.3.73data processing
BUSTER2.11.8refinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H19

5h19


Resolution: 1.602→15.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2266 -RANDOM
Rwork0.1818 ---
obs0.183 43528 79.6 %-
Displacement parametersBiso mean: 23.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.0571 Å20 Å20 Å2
2--2.8609 Å20 Å2
3----0.8038 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.602→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 31 290 3408
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083225HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974368HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1133SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3225HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2775SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion14.79
LS refinement shellResolution: 1.602→1.62 Å
RfactorNum. reflection% reflection
Rfree0.3269 48 -
Rwork0.2686 --
obs--43.67 %
Refinement TLS params.

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)
10.8397-0.07-0.27820.1219-0.06331.5054-0.091-0.03930.0101-0.0393-0.00830.00140.01010.00140.0993-0.05960.0167-0.0063-0.00190.0177-0.020513.178419.482421.2929
22.7201-3.07660.04796.5135-1.11242.0188-0.1190.0632-0.44820.06320.0060.5406-0.44820.54060.113-0.1096-0.031-0.04390.07050.0127-0.047125.308829.206930.0821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|78-440}A78 - 440
2X-RAY DIFFRACTION1{ A| 504 }A504
3X-RAY DIFFRACTION2{ B|* }B40 - 68

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