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- PDB-6ony: BRD2_Bromodomain1 complex with inhibitor 744 -

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Basic information

Entry
Database: PDB / ID: 6ony
TitleBRD2_Bromodomain1 complex with inhibitor 744
ComponentsBromodomain-containing protein 2
KeywordsSIGNALING PROTEIN / BRD2 / inhibitor
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HWV / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLongenecker, K.L. / Bigelow, L.
CitationJournal: Nature / Year: 2020
Title: Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancer.
Authors: Faivre, E.J. / McDaniel, K.F. / Albert, D.H. / Mantena, S.R. / Plotnik, J.P. / Wilcox, D. / Zhang, L. / Bui, M.H. / Sheppard, G.S. / Wang, L. / Sehgal, V. / Lin, X. / Huang, X. / Lu, X. / ...Authors: Faivre, E.J. / McDaniel, K.F. / Albert, D.H. / Mantena, S.R. / Plotnik, J.P. / Wilcox, D. / Zhang, L. / Bui, M.H. / Sheppard, G.S. / Wang, L. / Sehgal, V. / Lin, X. / Huang, X. / Lu, X. / Uziel, T. / Hessler, P. / Lam, L.T. / Bellin, R.J. / Mehta, G. / Fidanze, S. / Pratt, J.K. / Liu, D. / Hasvold, L.A. / Sun, C. / Panchal, S.C. / Nicolette, J.J. / Fossey, S.L. / Park, C.H. / Longenecker, K. / Bigelow, L. / Torrent, M. / Rosenberg, S.H. / Kati, W.M. / Shen, Y.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8786
Polymers29,7712
Non-polymers1,1074
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-12 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.662, 56.071, 106.981
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 Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 14885.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HWV / N-ethyl-4-[2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl]-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide


Mass: 491.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.665 M Ammonium Tartrate, 0.095 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.975→53.491 Å / Num. obs: 20711 / % possible obs: 97.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 1.975→2.009 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1032 / Rpim(I) all: 0.386 / % possible all: 96.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→53.49 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1029 4.97 %RANDOM
Rwork0.198 ---
obs0.2 20710 97.6 %-
Displacement parametersBiso max: 130.01 Å2 / Biso mean: 50.67 Å2 / Biso min: 29.49 Å2
Baniso -1Baniso -2Baniso -3
1-12.1965 Å20 Å20 Å2
2--14.8874 Å20 Å2
3----27.0839 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 1.98→53.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 80 132 2087
Biso mean--45.01 58.86 -
Num. residues----224
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d699SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes393HARMONIC5
X-RAY DIFFRACTIONt_it2009HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion243SEMIHARMONIC5
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_contact2390SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2009HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2725HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion19.76
LS refinement shellResolution: 1.98→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2663 17 4.1 %
Rwork0.2921 398 -
all0.2912 415 -
obs--95.88 %

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