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- PDB-7jkz: Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) compl... -

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Basic information

Entry
Database: PDB / ID: 7jkz
TitleBromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with YF3-126
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Selective BRD4-BD1 inhibitor
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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-YF6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsRatia, K.M. / Xiong, R. / Li, Y. / Shen, Z. / Zhao, J. / Huang, F. / Dubrovyskyii, O. / Thatcher, G.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)UL1RR029879 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Novel Pyrrolopyridone Bromodomain and Extra-Terminal Motif (BET) Inhibitors Effective in Endocrine-Resistant ER+ Breast Cancer with Acquired Resistance to Fulvestrant and Palbociclib.
Authors: Li, Y. / Zhao, J. / Gutgesell, L.M. / Shen, Z. / Ratia, K. / Dye, K. / Dubrovskyi, O. / Zhao, H. / Huang, F. / Tonetti, D.A. / Thatcher, G.R.J. / Xiong, R.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,8264
Polymers15,0601
Non-polymers7663
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.010, 63.010, 102.722
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15060.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-YF6 / N-(1-[1,1-di(pyridin-2-yl)ethyl]-6-{1-methyl-6-oxo-5-[(piperidin-4-yl)amino]-1,6-dihydropyridin-3-yl}-1H-indol-4-yl)ethanesulfonamide


Mass: 611.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1M Na cacodylate pH 6.5, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.49→54.57 Å / Num. obs: 8677 / % possible obs: 99.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 16.3
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 958 / Rpim(I) all: 0.147 / Rrim(I) all: 0.466 / Χ2: 0.85 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUO

2ouo


Resolution: 2.49→54.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.741 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 452 5.2 %RANDOM
Rwork0.18 ---
obs0.1816 8193 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.5 Å2 / Biso mean: 50.905 Å2 / Biso min: 34.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.57 Å20 Å2
2--1.14 Å20 Å2
3----3.7 Å2
Refinement stepCycle: final / Resolution: 2.49→54.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 54 34 993
Biso mean--52.2 51.5 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013989
X-RAY DIFFRACTIONr_bond_other_d0.0010.017915
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6561332
X-RAY DIFFRACTIONr_angle_other_deg1.3431.5872127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46822.44949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28715174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.747155
X-RAY DIFFRACTIONr_chiral_restr0.0870.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
LS refinement shellResolution: 2.491→2.556 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 20 -
Rwork0.237 590 -
all-610 -
obs--99.84 %

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