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- PDB-5u28: BRD4 first bromodomain (BD1) in complex with dual PI3 kinase inhi... -

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Basic information

Entry
Database: PDB / ID: 5u28
TitleBRD4 first bromodomain (BD1) in complex with dual PI3 kinase inhibitor SF2523
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / bromodomain / transcription / inhibitor / epigenetics / TRANSCRIPTION REGULATOR-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-82V / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsAndrews, F.H. / Kutateladze, T.G.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis.
Authors: Andrews, F.H. / Singh, A.R. / Joshi, S. / Smith, C.A. / Morales, G.A. / Garlich, J.R. / Durden, D.L. / Kutateladze, T.G.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,7744
Polymers16,2391
Non-polymers5363
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.972, 59.151, 63.675
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: 16238.729 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 (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-82V / 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one


Mass: 371.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17NO5S
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 40% PEG3350 (w/v) and 0.2 M potassium thiocyanate (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.798→28.035 Å / Num. obs: 15802 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 41.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DW2

5dw2


Resolution: 1.798→28.035 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.02
RfactorNum. reflection% reflection
Rfree0.223 1571 9.94 %
Rwork0.1785 --
obs0.183 15802 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.798→28.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 36 150 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011200
X-RAY DIFFRACTIONf_angle_d1.1081634
X-RAY DIFFRACTIONf_dihedral_angle_d15.167468
X-RAY DIFFRACTIONf_chiral_restr0.038171
X-RAY DIFFRACTIONf_plane_restr0.004211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7979-1.8560.25411160.17791162X-RAY DIFFRACTION90
1.856-1.92230.27811400.20241279X-RAY DIFFRACTION100
1.9223-1.99920.26161470.18441290X-RAY DIFFRACTION100
1.9992-2.09020.20531440.17551279X-RAY DIFFRACTION100
2.0902-2.20030.23541400.1851295X-RAY DIFFRACTION99
2.2003-2.33810.24081410.18961287X-RAY DIFFRACTION100
2.3381-2.51860.23441490.19351283X-RAY DIFFRACTION100
2.5186-2.77180.26851390.19171337X-RAY DIFFRACTION100
2.7718-3.17240.23541490.19851301X-RAY DIFFRACTION100
3.1724-3.99510.21371530.16271332X-RAY DIFFRACTION99
3.9951-28.0380.16621530.15711386X-RAY DIFFRACTION98

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