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- PDB-7p3c: EED in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 7p3c
TitleEED in complex with compound 4
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-51A / Chem-L9W / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsRead, J.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Diverse, Potent, and Efficacious Inhibitors That Target the EED Subunit of the Polycomb Repressive Complex 2 Methyltransferase.
Authors: Bagal, S.K. / Gregson, C. / O' Donovan, D.H. / Pike, K.G. / Bloecher, A. / Barton, P. / Borodovsky, A. / Code, E. / Fillery, S.M. / Hsu, J.H. / Kawatkar, S.P. / Li, C. / Longmire, D. / Nai, ...Authors: Bagal, S.K. / Gregson, C. / O' Donovan, D.H. / Pike, K.G. / Bloecher, A. / Barton, P. / Borodovsky, A. / Code, E. / Fillery, S.M. / Hsu, J.H. / Kawatkar, S.P. / Li, C. / Longmire, D. / Nai, Y. / Nash, S.C. / Pike, A. / Robinson, J. / Read, J.A. / Rawlins, P.B. / Shen, M. / Tang, J. / Wang, P. / Woods, H. / Williamson, B.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4244
Polymers84,5982
Non-polymers8262
Water12,863714
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
MethodPISA
2
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7042
Polymers42,2991
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.137, 89.151, 97.864
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-51A / N-[5-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methylamino]-[1,2,4]triazolo[4,3-c]pyrimidin-8-yl]benzamide


Mass: 404.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 298 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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.61→97.82 Å / Num. obs: 98092 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 23.53 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Net I/σ(I): 10.2 / Num. measured all: 624827 / Scaling rejects: 169
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.61-1.655.41.64871610.5570.782
7.2-1060.05312520.8380.0270.06

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SFB

6sfb


Resolution: 1.61→23.57 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.085
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4839 5.06 %RANDOM
Rwork0.178 ---
obs0.18 95686 97.7 %-
Displacement parametersBiso max: 125.19 Å2 / Biso mean: 30.8 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.6243 Å20 Å20 Å2
2---2.3287 Å20 Å2
3----0.2957 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.61→23.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 80 714 6296
Biso mean--23.84 43.7 -
Num. residues----694
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1938SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes835HARMONIC5
X-RAY DIFFRACTIONt_it5737HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion738SEMIHARMONIC5
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_contact6868SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5737HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7800HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion16.64
LS refinement shellResolution: 1.61→1.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 347 5.51 %
Rwork0.275 5951 -
all0.276 6298 -
obs--88.02 %
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)
11.1633-0.38090.02871.08660.24730.78780.00460.11170.0366-0.1182-0.0590.0214-0.0453-0.03650.0544-0.0661-0.0038-0.0176-0.0137-0.0212-0.056525.785333.98696.5185
22.92080.06490.56490.5649-0.05891.14480.0686-0.07890.05450.0573-0.0399-0.0171-0.03860.1377-0.0288-0.0718-0.0439-0.0095-0.0401-0.0381-0.0655-23.685943.486617.8379
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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