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- PDB-6czu: BRD4(BD1) complexed with 3219 -

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Basic information

Entry
Database: PDB / ID: 6czu
TitleBRD4(BD1) complexed with 3219
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION/INHIBITOR / Bromodomain / BRD4 / TRANSCRIPTION-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-FP7 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.47 Å
AuthorsLakshminarasimhan, D. / White, A. / Suto, R.K.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Design and Characterization of Novel Covalent Bromodomain and Extra-Terminal Domain (BET) Inhibitors Targeting a Methionine.
Authors: Kharenko, O.A. / Patel, R.G. / Brown, S.D. / Calosing, C. / White, A. / Lakshminarasimhan, D. / Suto, R.K. / Duffy, B.C. / Kitchen, D.B. / McLure, K.G. / Hansen, H.C. / van der Horst, E.H. / Young, P.R.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)16,16710
Polymers15,3301
Non-polymers8379
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.066, 48.967, 59.880
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 4 / BRD4 / Protein HUNK1


Mass: 15329.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: PJEXPRESS401 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-FP7 / 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-({4-[(1R)-1-hydroxyethyl]phenyl}methyl)pyridin-2(1H)-one


Mass: 324.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 22125 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.129 / Χ2: 1.078 / Net I/σ(I): 17 / Num. measured all: 148794
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.47-1.526.60.48321681.1711100
1.52-1.586.70.3821871.1251100
1.58-1.666.70.28321611.0771100
1.66-1.746.80.23421831.0921100
1.74-1.856.80.18821831.091100
1.85-26.80.15221971.0661100
2-2.26.90.1322101.0351100
2.2-2.516.80.12822291.0631100
2.51-3.176.70.1222451.0751100
3.17-506.50.10923620.995199

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 1.47→32.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.17 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.076
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1112 5 %RANDOM
Rwork0.1449 ---
obs0.1474 20962 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.25 Å2 / Biso mean: 17.079 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.47→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 64 216 1358
Biso mean--24.48 31.92 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021236
X-RAY DIFFRACTIONr_bond_other_d0.0030.021197
X-RAY DIFFRACTIONr_angle_refined_deg2.2462.0121673
X-RAY DIFFRACTIONr_angle_other_deg2.22832769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1826.03458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.094153
X-RAY DIFFRACTIONr_chiral_restr0.1330.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02272
LS refinement shellResolution: 1.472→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 79 -
Rwork0.205 1508 -
all-1587 -
obs--99.5 %

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