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- PDB-5u8a: Polycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bro... -

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Basic information

Entry
Database: PDB / ID: 5u8a
TitlePolycomb protein EED in complex with inhibitor: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine
ComponentsPolycomb protein EED
KeywordsPROTEIN BINDING/INHIBITOR / WD40 PRC2 / PROTEIN BINDING-INHIBITOR complex
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / sex chromatin / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / chromatin silencing complex / pronucleus / spinal cord development / Transcriptional Regulation by E2F6 / : ...regulation of adaxial/abaxial pattern formation / sex chromatin / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / chromatin silencing complex / pronucleus / spinal cord development / Transcriptional Regulation by E2F6 / : / oligodendrocyte differentiation / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / enzyme activator activity / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / heterochromatin formation / 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
: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-82D / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsJakob, C.G. / Zhu, H.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: SAR of amino pyrrolidines as potent and novel protein-protein interaction inhibitors of the PRC2 complex through EED binding.
Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / ...Authors: Curtin, M.L. / Pliushchev, M.A. / Li, H.Q. / Torrent, M. / Dietrich, J.D. / Jakob, C.G. / Zhu, H. / Zhao, H. / Wang, Y. / Ji, Z. / Clark, R.F. / Sarris, K.A. / Selvaraju, S. / Shaw, B. / Algire, M.A. / He, Y. / Richardson, P.L. / Sweis, R.F. / Sun, C. / Chiang, G.G. / Michaelides, M.R.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0142
Polymers42,5831
Non-polymers4301
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.768, 85.142, 91.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42583.484 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-82D / (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine


Mass: 430.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25BrFN3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8.5
Details: 3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→91.443 Å / Num. obs: 80241 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.8
Reflection shellResolution: 1.452→1.457 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.728 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K0M

5k0m


Resolution: 1.45→62.31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.877 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17318 4021 5 %RANDOM
Rwork0.15094 ---
obs0.15203 76142 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.45→62.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 27 226 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193002
X-RAY DIFFRACTIONr_bond_other_d0.0020.022697
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9394070
X-RAY DIFFRACTIONr_angle_other_deg0.96136260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79523.878147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48815513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3191519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02651
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.2661431
X-RAY DIFFRACTIONr_mcbond_other0.8121.2641430
X-RAY DIFFRACTIONr_mcangle_it0.9561.9041787
X-RAY DIFFRACTIONr_mcangle_other0.9571.9051788
X-RAY DIFFRACTIONr_scbond_it1.4221.5911571
X-RAY DIFFRACTIONr_scbond_other1.4211.5911572
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4212.2582284
X-RAY DIFFRACTIONr_long_range_B_refined1.72215.5553307
X-RAY DIFFRACTIONr_long_range_B_other1.56215.3383273
X-RAY DIFFRACTIONr_rigid_bond_restr1.55735699
X-RAY DIFFRACTIONr_sphericity_free13.9335154
X-RAY DIFFRACTIONr_sphericity_bonded3.18855694
LS refinement shellResolution: 1.452→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 314 -
Rwork0.252 5516 -
obs--99.79 %

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