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- PDB-5uey: BRD4_BD2_A-1412838 -

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Basic information

Entry
Database: PDB / ID: 5uey
TitleBRD4_BD2_A-1412838
ComponentsBromodomain-containing protein 4BRD4
KeywordsSIGNALING PROTEIN/INHIBITOR / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-88M / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.41 Å
AuthorsPark, C.H.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors.
Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, ...Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, T.M. / Hubbard, R. / Park, C.H. / Li, L. / Magoc, T.J. / Albert, D.H. / Lin, X. / Warder, S.E. / Kovar, P. / Huang, X. / Wilcox, D. / Wang, R. / Rajaraman, G. / Petros, A.M. / Hutchins, C.W. / Panchal, S.C. / Sun, C. / Elmore, S.W. / Shen, Y. / Kati, W.M. / McDaniel, K.F.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Mar 6, 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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2732
Polymers12,8071
Non-polymers4661
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.185, 74.627, 33.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 12806.933 Da / Num. of mol.: 1 / Fragment: residues 352-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O60885
#2: Chemical ChemComp-88M / 5-[2-(2,4-difluorophenoxy)-5-{[ethyl(dihydroxy)-lambda~4~-sulfanyl]amino}phenyl]-4-ethoxy-1-methylpyridin-2(1H)-one


Mass: 466.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24F2N2O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→33.4 Å / Num. obs: 5571 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 70 Å2 / Rsym value: 0.047 / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
Cootmodel building
BUSTER2.11.7refinement
RefinementResolution: 2.41→33.38 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.85 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.504 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.31 251 4.54 %RANDOM
Rwork0.27 ---
obs0.272 5523 98.6 %-
Displacement parametersBiso mean: 71.16 Å2
Baniso -1Baniso -2Baniso -3
1--31.7893 Å20 Å20 Å2
2--26.1272 Å20 Å2
3---5.6622 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 2.41→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 32 30 909
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008913HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.921242HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d300SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes18HARMONIC2
X-RAY DIFFRACTIONt_gen_planes146HARMONIC5
X-RAY DIFFRACTIONt_it913HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.52
X-RAY DIFFRACTIONt_other_torsion21.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion110SEMIHARMONIC5
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_contact992SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.398 -5.44 %
Rwork0.356 1426 -
all0.359 1508 -
obs--97.92 %

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