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- PDB-4hxp: Brd4 Bromodomain 1 complex with 4-(2-OXO-1,3-OXAZOLIDIN-3-YL)BENZ... -

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Basic information

Entry
Database: PDB / ID: 4hxp
TitleBrd4 Bromodomain 1 complex with 4-(2-OXO-1,3-OXAZOLIDIN-3-YL)BENZAMIDE inhibitor
ComponentsBromodomain-containing protein 4
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 / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
4-(2-oxo-1,3-oxazolidin-3-yl)benzamide / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9602
Polymers14,7541
Non-polymers2061
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.310, 47.420, 78.960
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 / 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-1A5 / 4-(2-oxo-1,3-oxazolidin-3-yl)benzamide


Mass: 206.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.05 Å3/Da / Density % sol: 40 %
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: Mar 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→39.48 Å / Num. obs: 24428 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.99 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.73-1.770.5122.625722180398.8
1.77-1.820.4353.536552178599.9
1.82-1.880.3824.056436168699.9
1.88-1.930.3035.166407167499.9
1.93-20.2436.1762551632100
2-2.070.1698.2958171526100
2.07-2.150.1499.495867152799.9
2.15-2.230.11811.455542144699.9
2.23-2.330.10412.475388140199.9
2.33-2.450.09713.245084132699.9
2.45-2.580.08215.684770124499.8
2.58-2.740.0717.634641121199.8
2.74-2.920.05720.394263111799.8
2.92-3.160.0522.883958104699.6
3.16-3.460.04226.41353094199.8
3.46-3.870.03831.02330688499.5
3.87-4.470.03432.29283576799.9
4.47-5.470.03232.61239764399.7
5.47-7.740.02930.86192550099.8
7.740.02534.6998726998.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.48 Å
Translation2.5 Å39.48 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→39.48 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8669 / SU ML: 0.19 / σ(F): 1.31 / Phase error: 20.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1932 732 3 %
Rwork0.1706 --
obs0.1713 24428 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.46 Å2 / Biso mean: 14.7356 Å2 / Biso min: 5.09 Å2
Refinement stepCycle: LAST / Resolution: 1.73→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 15 116 1164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061086
X-RAY DIFFRACTIONf_angle_d1.0761480
X-RAY DIFFRACTIONf_chiral_restr0.069156
X-RAY DIFFRACTIONf_plane_restr0.005192
X-RAY DIFFRACTIONf_dihedral_angle_d12.514433
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 (%)
1.73-1.86360.23521460.2164727487399
1.8636-2.05110.22681490.177847664915100
2.0511-2.34780.21011470.162347104857100
2.3478-2.95790.17121440.180247784922100
2.9579-39.49030.17911460.156647154861100

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