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- PDB-4hxr: 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: 4hxr
TitleBrd4 Bromodomain 1 complex with N-[3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)PHENYL]THIOPHENE-2-SULFONAMIDE 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
Chem-1A4 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 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)15,2222
Polymers14,8831
Non-polymers3381
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.280, 47.280, 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 / 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-1A4 / N-[3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)phenyl]thiophene-2-sulfonamide


Mass: 338.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O3S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
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: 1.53→40.557 Å / Num. obs: 18865 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.348 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.53-1.570.5334.2686371365100
1.57-1.610.4634.9685671356100
1.61-1.660.4075.6580371263100
1.66-1.710.3666.48106128499.9
1.71-1.770.3077.427744121999.9
1.77-1.830.2499.0475551192100
1.83-1.90.22510.077373116299.9
1.9-1.980.16813.0669981103100
1.98-2.060.13415.596660105299.9
2.06-2.160.10618.466588103699.9
2.16-2.280.08921.886127970100
2.28-2.420.0823.39572591299.9
2.42-2.590.07225.23548887399.7
2.59-2.790.0629.11512182299.8
2.79-3.060.05132.4459175399.6
3.06-3.420.04237.35417468999.4
3.42-3.950.03443.28357161199.3
3.95-4.840.02946.023184527100
4.84-6.840.02941.012473423100
6.840.02843.35130525398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.56 Å
Translation2.5 Å40.56 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: 1.53→40.557 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8837 / SU ML: 0.1 / σ(F): 2 / Phase error: 18.05 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1989 566 3 %
Rwork0.1728 --
obs0.1735 18865 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.35 Å2 / Biso mean: 12.7174 Å2 / Biso min: 4.45 Å2
Refinement stepCycle: LAST / Resolution: 1.53→40.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 21 135 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061104
X-RAY DIFFRACTIONf_angle_d1.1531508
X-RAY DIFFRACTIONf_chiral_restr0.08159
X-RAY DIFFRACTIONf_plane_restr0.005193
X-RAY DIFFRACTIONf_dihedral_angle_d16.672433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.53-1.68390.19091390.168544984637
1.6839-1.92760.21371390.175444974636
1.9276-2.42850.19531410.172145644705
2.4285-40.57150.19781470.173447404887

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