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- PDB-4hxo: Brd4 Bromodomain 1 complex with 3-{[(3-METHYL-1,2-OXAZOL-5-YL)MET... -

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Basic information

Entry
Database: PDB / ID: 4hxo
TitleBrd4 Bromodomain 1 complex with 3-{[(3-METHYL-1,2-OXAZOL-5-YL)METHYL]SULFANYL}[1,2,4]TRIAZOLO[4,3-A]PYRIDINE 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 / 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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 II / Brdt, bromodomain, repeat I / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1A6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 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 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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)15,1292
Polymers14,8831
Non-polymers2461
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.400, 47.580, 78.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-1A6 / 3-{[(3-methyl-1,2-oxazol-5-yl)methyl]sulfanyl}[1,2,4]triazolo[4,3-a]pyridine


Mass: 246.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N4OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 39.35 %
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: 1.76→30.24 Å / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.58
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.76-1.810.5254.16199.8
1.81-1.860.4424.69198.9
1.86-1.910.3655.48199
1.91-1.970.3185.98199.9
1.97-2.030.2517.21199.3
2.03-2.10.1818.82199.2
2.1-2.180.1619.55199.7
2.18-2.270.13510.79199.6
2.27-2.370.12911.13199.9
2.37-2.490.11811.69199.8
2.49-2.620.09713.28199.8
2.62-2.780.08814.03199.9
2.78-2.980.07416.17199.8
2.98-3.210.06317.971100
3.21-3.520.05620.24199.7
3.52-3.940.0522.36199.8
3.94-4.540.04524.231100
4.54-5.570.04723.741100
5.57-7.870.04322.521100
7.870.03525.25196.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.24 Å
Translation2.5 Å30.24 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→30.24 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.344 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22918 375 3 %RANDOM
Rwork0.16849 ---
obs0.17024 12125 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.766 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2---0.89 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 17 93 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9891480
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0685124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49125.68651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.369153
X-RAY DIFFRACTIONr_chiral_restr0.1520.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022831
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 25 -
Rwork0.191 783 -
obs--99.63 %

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