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- PDB-5ls6: Structure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ls6
TitleStructure of Human Polycomb Repressive Complex 2 (PRC2) with inhibitor
Components
  • (Polycomb protein ...) x 2
  • Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
  • Jarid2 K116me3
KeywordsTransferase/Inhibitor / Human PRC2 / Inhibitor / H3K27 / Transferase-Inhibitor complex
Function / homology
Function and homology information


protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity ...protein localization to pericentric heterochromatin / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / primary miRNA binding / random inactivation of X chromosome / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / regulatory ncRNA-mediated heterochromatin formation / negative regulation of cardiac muscle cell proliferation / histone H3K27 methyltransferase activity / sex chromatin / ubiquitin-modified histone reader activity / positive regulation of cell cycle G1/S phase transition / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / negative regulation of stem cell differentiation / RSC-type complex / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/3 reader activity / chromatin silencing complex / pronucleus / positive regulation of dendrite development / G1 to G0 transition / histone H3 methyltransferase activity / histone methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / lncRNA binding / negative regulation of gene expression, epigenetic / synaptic transmission, GABAergic / Transcriptional Regulation by E2F6 / : / positive regulation of MAP kinase activity / histone methyltransferase complex / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / positive regulation of GTPase activity / positive regulation of protein serine/threonine kinase activity / negative regulation of cell differentiation / cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / subtelomeric heterochromatin formation / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / keratinocyte differentiation / spleen development / protein localization to chromatin / liver regeneration / negative regulation of cytokine production involved in inflammatory response / SUMOylation of chromatin organization proteins / thymus development / cellular response to leukemia inhibitory factor / B cell differentiation / central nervous system development / ubiquitin binding / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / hippocampus development / stem cell differentiation / promoter-specific chromatin binding / enzyme activator activity / liver development / G1/S transition of mitotic cell cycle / protein-DNA complex / regulation of circadian rhythm / chromatin DNA binding / protein modification process / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / rhythmic process / transcription corepressor activity / response to estradiol / heterochromatin formation / chromosome / chromatin organization / regulation of gene expression / Oxidative Stress Induced Senescence / histone binding / methylation / chromosome, telomeric region / cell population proliferation / nuclear body
Similarity search - Function
Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / 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 ...Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / 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 / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / : / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / JmjC domain, hydroxylase / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / SANT/Myb domain / Zinc finger C2H2 type domain signature. / 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-74D / Polycomb protein EED / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2 / Protein Jumonji
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsZhang, Y. / Justin, N. / Chen, S. / Wilson, J. / Gamblin, S.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and ...Title: Identification of (R)-N-((4-Methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1-(1-(1-(2,2,2-trifluoroethyl)piperidin-4-yl)ethyl)-1H-indole-3-carboxamide (CPI-1205), a Potent and Selective Inhibitor of Histone Methyltransferase EZH2, Suitable for Phase I Clinical Trials for B-Cell Lymphomas.
Authors: Vaswani, R.G. / Gehling, V.S. / Dakin, L.A. / Cook, A.S. / Nasveschuk, C.G. / Duplessis, M. / Iyer, P. / Balasubramanian, S. / Zhao, F. / Good, A.C. / Campbell, R. / Lee, C. / Cantone, N. / ...Authors: Vaswani, R.G. / Gehling, V.S. / Dakin, L.A. / Cook, A.S. / Nasveschuk, C.G. / Duplessis, M. / Iyer, P. / Balasubramanian, S. / Zhao, F. / Good, A.C. / Campbell, R. / Lee, C. / Cantone, N. / Cummings, R.T. / Normant, E. / Bellon, S.F. / Albrecht, B.K. / Harmange, J.C. / Trojer, P. / Audia, J.E. / Zhang, Y. / Justin, N. / Chen, S. / Wilson, J.R. / Gamblin, S.J.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
B: Polycomb protein EED
C: Polycomb protein SUZ12
D: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
E: Polycomb protein EED
F: Polycomb protein SUZ12
G: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
H: Polycomb protein EED
I: Polycomb protein SUZ12
J: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
K: Polycomb protein EED
L: Polycomb protein SUZ12
Q: Jarid2 K116me3
R: Jarid2 K116me3
S: Jarid2 K116me3
T: Jarid2 K116me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)557,89452
Polymers553,74316
Non-polymers4,15236
Water00
1
A: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
B: Polycomb protein EED
C: Polycomb protein SUZ12
Q: Jarid2 K116me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,47413
Polymers138,4364
Non-polymers1,0389
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
E: Polycomb protein EED
F: Polycomb protein SUZ12
R: Jarid2 K116me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,47413
Polymers138,4364
Non-polymers1,0389
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
H: Polycomb protein EED
I: Polycomb protein SUZ12
S: Jarid2 K116me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,47413
Polymers138,4364
Non-polymers1,0389
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2
K: Polycomb protein EED
L: Polycomb protein SUZ12
T: Jarid2 K116me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,47413
Polymers138,4364
Non-polymers1,0389
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.310, 170.270, 275.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Polycomb protein ... , 2 types, 8 molecules BEHKCFIL

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


Mass: 42314.145 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O75530
#3: Protein
Polycomb protein SUZ12 / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 15249.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15022

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Protein / Protein/peptide , 2 types, 8 molecules ADGJQRST

#1: Protein
Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2,Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 79494.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q15910, histone-lysine N-methyltransferase
#4: Protein/peptide
Jarid2 K116me3


Mass: 1377.614 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92833*PLUS

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Non-polymers , 2 types, 36 molecules

#5: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-74D / 1-[(1~{R})-1-[1-[2,2-bis(fluoranyl)propyl]piperidin-4-yl]ethyl]-~{N}-[(4-methoxy-6-methyl-2-oxidanylidene-3~{H}-pyridin-3-yl)methyl]-2-methyl-indole-3-carboxamide


Mass: 514.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H36F2N4O3

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.67 / Details: 24% PEG3350, 400mM Ammonian Citrate pH6.67 / PH range: 6.5-6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.47→68.84 Å / Num. obs: 76561 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.3 / Net I/σ(I): 6.9
Reflection shellResolution: 3.47→3.56 Å / Redundancy: 7 % / Rmerge(I) obs: 1.81 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.63 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HYN

5hyn


Resolution: 3.47→68.84 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.856 / SU B: 50.578 / SU ML: 0.715 / Cross valid method: THROUGHOUT / ESU R Free: 0.712 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29866 3952 4.9 %RANDOM
Rwork0.22867 ---
obs0.23215 76561 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 104.386 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--7.94 Å2-0 Å2
3----6.28 Å2
Refinement stepCycle: 1 / Resolution: 3.47→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34711 0 180 0 34891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01935667
X-RAY DIFFRACTIONr_bond_other_d0.0030.0233400
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.94648152
X-RAY DIFFRACTIONr_angle_other_deg1.1013.00276964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.06354246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85724.0481801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.322156315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.57415252
X-RAY DIFFRACTIONr_chiral_restr0.1280.25102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02140260
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028584
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_it6.02410.40317092
X-RAY DIFFRACTIONr_mcbond_other6.02410.40217091
X-RAY DIFFRACTIONr_mcangle_it10.0715.57321302
X-RAY DIFFRACTIONr_mcangle_other10.0715.57321303
X-RAY DIFFRACTIONr_scbond_it4.98510.58518575
X-RAY DIFFRACTIONr_scbond_other4.98510.58518575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.77715.77726851
X-RAY DIFFRACTIONr_long_range_B_refined14.59280.43439765
X-RAY DIFFRACTIONr_long_range_B_other14.59180.43639766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.47→3.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 280 -
Rwork0.385 5594 -
obs--99.9 %

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