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- PDB-6yvj: EED in complex with a triazolopyrimidine -

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Basic information

Entry
Database: PDB / ID: 6yvj
TitleEED in complex with a triazolopyrimidine
ComponentsPolycomb protein EED
KeywordsPROTEIN BINDING / Methyl transferase EED PRC2 epigenetic H3K27 WD40 inhibitor
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 / PKMTs methylate histone lysines ...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 / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-EJR / Chem-L9W / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsRead, J.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Free energy perturbation in the design of EED ligands as inhibitors of polycomb repressive complex 2 (PRC2) methyltransferase.
Authors: O' Donovan, D.H. / Gregson, C. / Packer, M.J. / Greenwood, R. / Pike, K.G. / Kawatkar, S. / Bloecher, A. / Robinson, J. / Read, J. / Code, E. / Hsu, J.H. / Shen, M. / Woods, H. / Barton, P. ...Authors: O' Donovan, D.H. / Gregson, C. / Packer, M.J. / Greenwood, R. / Pike, K.G. / Kawatkar, S. / Bloecher, A. / Robinson, J. / Read, J. / Code, E. / Hsu, J.H. / Shen, M. / Woods, H. / Barton, P. / Fillery, S. / Williamson, B. / Rawlins, P.B. / Bagal, S.K.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_refine_tls_group
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_refine_tls_group.selection_details
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4885
Polymers84,5982
Non-polymers8903
Water10,359575
1
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7212
Polymers42,2991
Non-polymers4211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7683
Polymers42,2991
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.020, 89.870, 99.140
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: 42299.195 Da / Num. of mol.: 2
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-L9W / N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine


Mass: 421.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N5O3S
#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-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.: 575 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.1M PCTP pH7.7, 130mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.84→44.94 Å / Num. obs: 68048 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Net I/σ(I): 14.3 / Num. measured all: 449506
Reflection shell

Num. unique obs: 4957 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) all% possible allRmerge(I) obsMean I/σ(I) obs
1.84-1.896.80.5860.7899.7
1.84-1.96.80.5999.71.61.2

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
BUSTERrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SFB

6sfb


Resolution: 1.84→44.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.11
RfactorNum. reflection% reflectionSelection details
Rfree0.199 3351 4.93 %RANDOM
Rwork0.182 ---
obs0.182 67959 99.8 %-
Displacement parametersBiso max: 130.88 Å2 / Biso mean: 39.23 Å2 / Biso min: 16.31 Å2
Baniso -1Baniso -2Baniso -3
1-9.0644 Å20 Å20 Å2
2---8.361 Å20 Å2
3----0.7034 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.84→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5509 0 92 575 6176
Biso mean--29.87 49.7 -
Num. residues----694
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1955SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it5784HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion742SEMIHARMONIC5
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_contact6048SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5784HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7866HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion16.84
LS refinement shellResolution: 1.84→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 231 4.68 %
Rwork0.304 4706 -
all0.305 4937 -
obs--99.44 %
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)
11.5584-0.3487-0.05451.14130.19270.8904-0.01150.14090.0476-0.0757-0.03630.0296-0.0188-0.01630.0478-0.0785-0.0213-0.0248-0.0256-0.0429-0.092425.9734.50026.6206
23.39830.03130.78220.6514-0.01211.4763-0.02460.07850.04440.05050.0211-0.0312-0.09220.24330.0035-0.1149-0.05110.0024-0.052-0.0755-0.1184-24.057344.137617.8598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|82 - A|439 }A82 - 439
2X-RAY DIFFRACTION2{ B|81 - B|439 }B81 - 439

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