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- PDB-7oe8: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6r)-3-oxabic... -

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Basic information

Entry
Database: PDB / ID: 7oe8
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N5-((1R,5S,6r)-3-oxabicyclo[3.1.0]hexan-6-yl)-3-(1H-indol-4-yl)-N7-methyl-2,3-dihydrobenzofuran-5,7-dicarboxamide
ComponentsBromodomain-containing protein 2BRD2
KeywordsNUCLEAR PROTEIN / Inhibitor / Bromodomain
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / 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 ...chromatin looping / acetylation-dependent protein binding / 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 phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-V9Q / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.301 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Optimization of a Series of 2,3-Dihydrobenzofurans as Highly Potent, Second Bromodomain (BD2)-Selective, Bromo and Extra-Terminal Domain (BET) Inhibitors.
Authors: Lucas, S.C.C. / Atkinson, S.J. / Chung, C.W. / Davis, R. / Gordon, L. / Grandi, P. / Gray, J.J.R. / Grimes, T. / Phillipou, A. / Preston, A.G. / Prinjha, R.K. / Rioja, I. / Taylor, S. / ...Authors: Lucas, S.C.C. / Atkinson, S.J. / Chung, C.W. / Davis, R. / Gordon, L. / Grandi, P. / Gray, J.J.R. / Grimes, T. / Phillipou, A. / Preston, A.G. / Prinjha, R.K. / Rioja, I. / Taylor, S. / Tomkinson, N.C.O. / Wall, I. / Watson, R.J. / Woolven, J. / Demont, E.H.
History
DepositionMay 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 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: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9744
Polymers13,4321
Non-polymers5423
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint4 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.934, 52.389, 31.998
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13432.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-V9Q / (3S)-3-(1H-indol-4-yl)-N7-methyl-N5-[(1R,5S)-3-oxabicyclo[3.1.0]hexan-6-yl]-2,3-dihydro-1-benzofuran-5,7-dicarboxamide / N5-((1R,5S,6r)-3-oxabicyclo[3.1.0]hexan-6-yl)-3-(1H-indol-4-yl)-N7-methyl-2,3-dihydrobenzofuran-5,7-dicarboxamide


Mass: 417.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% PEG 300, 0.1M MES buffer pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→19.51 Å / Num. obs: 29361 / % possible obs: 96.6 % / Redundancy: 15.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.8
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3570 / CC1/2: 0.924 / % possible all: 82.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: in house model

Resolution: 1.301→19.51 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.063 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 1408 -RANDOM
Rwork0.2037 ---
obs0.2042 29329 96.3 %-
Displacement parametersBiso mean: 15.12 Å2
Baniso -1Baniso -2Baniso -3
1-2.1299 Å20 Å20 Å2
2--1.2341 Å20 Å2
3----3.364 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.301→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 39 164 1126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091009HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.851362HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d361SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes168HARMONIC5
X-RAY DIFFRACTIONt_it1009HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion116SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1018SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.35
X-RAY DIFFRACTIONt_other_torsion16.7
LS refinement shellResolution: 1.301→1.31 Å
RfactorNum. reflection% reflection
Rfree0.2212 20 -
Rwork0.2 --
obs--67.82 %

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