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- PDB-4hxn: Brd4 Bromodomain 1 complex with 4-(2-FLUOROPHENYL)-1,3-THIAZOL-2(... -

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Basic information

Entry
Database: PDB / ID: 4hxn
TitleBrd4 Bromodomain 1 complex with 4-(2-FLUOROPHENYL)-1,3-THIAZOL-2(3H)-ONE 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-fluorophenyl)-1,3-thiazol-2(3H)-one / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 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)15,0782
Polymers14,8831
Non-polymers1951
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.980, 47.150, 79.070
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: 14883.188 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-1A7 / 4-(2-fluorophenyl)-1,3-thiazol-2(3H)-one


Mass: 195.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6FNOS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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 Å3/Da / Density % sol: 38.58 %
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: 1.49→40.497 Å / Num. obs: 37588 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.726 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.49-1.530.2564.129596284299.9
1.53-1.570.2374.610077269699.9
1.57-1.620.215.239929265999.9
1.62-1.670.1875.849534253999.9
1.67-1.720.1686.493932500100
1.72-1.780.1527.089191243799.9
1.78-1.850.147.6887162313100
1.85-1.920.138.468373221499.9
1.92-2.010.129.428097214499.9
2.01-2.110.11210.277767205399.7
2.11-2.220.10710.9873721941100
2.22-2.360.10411.327000184499.8
2.36-2.520.10311.666525171599.8
2.52-2.720.10311.876181163399.9
2.72-2.980.09912.315577147499.8
2.98-3.330.09912.435029133799.6
3.33-3.850.09912.854361117999.5
3.85-4.710.09713360296896.3
4.71-6.660.09512.93282875798.3
6.660.10212.13117434382.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.5 Å
Translation2.5 Å40.5 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: 1.49→40.497 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8703 / SU ML: 0.13 / σ(F): 1.48 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1125 2.99 %
Rwork0.1762 --
obs0.1772 37585 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.21 Å2 / Biso mean: 15.3306 Å2 / Biso min: 5.95 Å2
Refinement stepCycle: LAST / Resolution: 1.49→40.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 13 129 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061092
X-RAY DIFFRACTIONf_angle_d1.1091488
X-RAY DIFFRACTIONf_chiral_restr0.075158
X-RAY DIFFRACTIONf_plane_restr0.005191
X-RAY DIFFRACTIONf_dihedral_angle_d14.34422
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4899-1.55770.2311410.18245814722100
1.5577-1.63990.22881440.170245644708100
1.6399-1.74260.21491450.166645844729100
1.7426-1.87710.27681390.178545904729100
1.8771-2.0660.20121370.167945294666100
2.066-2.3650.20571410.170446004741100
2.365-2.97950.2011400.189745654705100
2.9795-40.51160.20781380.1754447458597

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