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- PDB-5u2e: BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3... -

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Basic information

Entry
Database: PDB / ID: 5u2e
TitleBRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2535
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / bromodomain / transcription / inhibitor / epigenetics / TRANSCRIPTION REGULATOR-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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-837 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.991 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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5974
Polymers32,8262
Non-polymers7712
Water4,954275
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7982
Polymers16,4131
Non-polymers3851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7982
Polymers16,4131
Non-polymers3851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.943, 39.701, 62.470
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 16412.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60885
#2: Chemical ChemComp-837 / ethyl 4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzoate


Mass: 385.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19NO5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG3350 (w/v), 0.2 M ammonium chloride, 0.1 M TRIS

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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 300K / Detector: PIXEL / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→33.41 Å / Num. obs: 32646 / % possible obs: 99.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 39.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.991→33.354 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 3721 9.76 %
Rwork0.1959 --
obs0.2002 38138 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.991→33.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 54 275 2453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072260
X-RAY DIFFRACTIONf_angle_d0.9643081
X-RAY DIFFRACTIONf_dihedral_angle_d13.4621374
X-RAY DIFFRACTIONf_chiral_restr0.044320
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9915-2.01670.38871220.31981053X-RAY DIFFRACTION82
2.0167-2.04320.39081390.29381290X-RAY DIFFRACTION97
2.0432-2.07120.36641300.28171343X-RAY DIFFRACTION96
2.0712-2.10080.34811390.27521314X-RAY DIFFRACTION97
2.1008-2.13220.32371360.25351272X-RAY DIFFRACTION98
2.1322-2.16550.27611570.2381322X-RAY DIFFRACTION99
2.1655-2.2010.26981320.21971330X-RAY DIFFRACTION99
2.201-2.23890.28331520.23161325X-RAY DIFFRACTION98
2.2389-2.27960.28361460.22451281X-RAY DIFFRACTION98
2.2796-2.32340.28791420.23991315X-RAY DIFFRACTION98
2.3234-2.37090.25131430.23511335X-RAY DIFFRACTION98
2.3709-2.42240.24261430.22941278X-RAY DIFFRACTION98
2.4224-2.47870.23431420.20191367X-RAY DIFFRACTION98
2.4787-2.54070.25311380.2191268X-RAY DIFFRACTION97
2.5407-2.60940.22921430.21541311X-RAY DIFFRACTION97
2.6094-2.68610.40851390.22671264X-RAY DIFFRACTION96
2.6861-2.77280.23731320.22751257X-RAY DIFFRACTION95
2.7728-2.87180.28941340.21141312X-RAY DIFFRACTION94
2.8718-2.98670.28491360.22821251X-RAY DIFFRACTION94
2.9867-3.12260.23721290.20451278X-RAY DIFFRACTION95
3.1226-3.28710.23881480.19471294X-RAY DIFFRACTION96
3.2871-3.49280.20271450.1691287X-RAY DIFFRACTION97
3.4928-3.76220.18971340.16361258X-RAY DIFFRACTION95
3.7622-4.14010.23511400.14791267X-RAY DIFFRACTION94
4.1401-4.73780.20721220.14181201X-RAY DIFFRACTION90
4.7378-5.96350.16161280.17471134X-RAY DIFFRACTION85
5.9635-33.35850.2031300.18521210X-RAY DIFFRACTION90

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