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- PDB-3fpd: G9a-like protein lysine methyltransferase inhibition by BIX-01294 -

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Basic information

Entry
Database: PDB / ID: 3fpd
TitleG9a-like protein lysine methyltransferase inhibition by BIX-01294
ComponentsHistone-lysine N-methyltransferase, H3 lysine-9 specific 5
KeywordsTRANSFERASE / Epigenetics / Histone lysine methylation / catalytic SET domain / Inhibition by BIX-01294 / Alternative splicing / ANK repeat / Chromatin regulator / Metal-binding / Methyltransferase / Nucleus / Phosphoprotein / Polymorphism / S-adenosyl-L-methionine / Zinc
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / nuclear body / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT1 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain ...Histone-lysine N-methyltransferase EHMT1 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-Q4A / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, Y. / Zhang, X. / Horton, J.R. / Cheng, X.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.
Authors: Chang, Y. / Zhang, X. / Horton, J.R. / Upadhyay, A.K. / Spannhoff, A. / Liu, J. / Snyder, J.P. / Bedford, M.T. / Cheng, X.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_site
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_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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, H3 lysine-9 specific 5
B: Histone-lysine N-methyltransferase, H3 lysine-9 specific 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,73814
Polymers60,4652
Non-polymers2,27312
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-9 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 95.200, 101.700
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 Histone-lysine N-methyltransferase, H3 lysine-9 specific 5 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine N-methyltransferase ...Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP1 / Lysine N-methyltransferase 1D


Mass: 30232.373 Da / Num. of mol.: 2 / Fragment: UNP residues 975-1235, SET domain
Source method: isolated from a genetically manipulated source
Details: BIX-01294 purchased from ALEXIS / Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, KIAA1876, KMT1D / Plasmid: pXC681 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9B1, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-Q4A / N-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine


Mass: 490.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38N6O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 18-20 % polyethylene glycol 4000 and 7-10 % isopropanol, in the absence or presence of DMSO (6-36%), VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30.26 Å / Num. obs: 26244 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 / Num. unique all: 1995

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IGQ

2igq


Resolution: 2.4→30.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 270243.59 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1201 4.9 %RANDOM
Rwork0.221 ---
obs-24680 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0185 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.35 Å20 Å20 Å2
2---13.97 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-30.3 Å
Luzzati sigma a0.35 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 132 119 4425
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.402 52 4.2 %
Rwork0.398 1183 -
obs-1183 42.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top

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