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- PDB-4hxs: Brd4 Bromodomain 1 complex with N-[3-(2-OXO-2,3-DIHYDRO-1,3-THIAZ... -

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Basic information

Entry
Database: PDB / ID: 4hxs
TitleBrd4 Bromodomain 1 complex with N-[3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)PHENYL]-1-PHENYLMETHANESULFONAMIDE inhibitor
ComponentsBromodomain-containing protein 4BRD4
KeywordsPROTEIN BINDING/INHIBITOR / BRD4 / Bromodomain / four alpha helices / PROTEIN BINDING-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 T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / 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 T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / 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-1A3 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsChen, T.T. / Cao, D.Y. / Chen, W.Y. / Xiong, B. / Shen, J.K. / Xu, Y.C.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Fragment-Based Drug Discovery of 2-Thiazolidinones as Inhibitors of the Histone Reader BRD4 Bromodomain.
Authors: Zhao, L. / Cao, D. / Chen, T. / Wang, Y. / Miao, Z. / Xu, Y. / Chen, W. / Wang, X. / Li, Y. / Du, Z. / Xiong, B. / Li, J. / Xu, C. / Zhang, N. / He, J. / Shen, J.
History
DepositionNov 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Structure summary
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1002
Polymers14,7541
Non-polymers3461
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.140, 47.140, 78.910
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: 14754.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus / References: UniProt: O60885
#2: Chemical ChemComp-1A3 / N-[3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)phenyl]-1-phenylmethanesulfonamide


Mass: 346.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N2O3S2
#3: Water ChemComp-HOH / water / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→40.469 Å / Num. obs: 22659 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.891 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.43-1.470.14112.47118561676100
1.47-1.510.11515.0611407160199.9
1.51-1.550.116.68111821572100
1.55-1.60.08218.95109411535100
1.6-1.650.07321.54105891481100
1.65-1.710.06524.03103591454100
1.71-1.770.05826.51100561401100
1.77-1.850.05329.0895081334100
1.85-1.930.04632.4491421285100
1.93-2.020.04235.8388361244100
2.02-2.130.03939.4683961183100
2.13-2.260.03741.7478261110100
2.26-2.420.03742.937355105199.9
2.42-2.610.03744.076895995100
2.61-2.860.03645.67620691499.7
2.86-3.20.03445.74543783199.5
3.2-3.690.03445.93447973198.5
3.69-4.520.03244.64338158191.4
4.52-6.40.03243.72260846590.5
6.40.03839.19101921570.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.47 Å
Translation2.5 Å40.47 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→40.469 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.874 / SU ML: 0.1 / σ(F): 2 / Phase error: 18.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.204 680 3 %
Rwork0.1778 --
obs0.1786 22657 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.47 Å2 / Biso mean: 15.1415 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: LAST / Resolution: 1.43→40.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 23 132 1192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061097
X-RAY DIFFRACTIONf_angle_d1.1691496
X-RAY DIFFRACTIONf_chiral_restr0.073157
X-RAY DIFFRACTIONf_plane_restr0.005191
X-RAY DIFFRACTIONf_dihedral_angle_d13.858428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4301-1.54050.21271350.166143604495100
1.5405-1.69560.2131350.168143764511100
1.6956-1.94090.19841350.170943654500100
1.9409-2.44530.19361370.173744484585100
2.4453-40.48490.20861380.1874428456696

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