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- PDB-5u2c: BRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI... -

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Basic information

Entry
Database: PDB / ID: 5u2c
TitleBRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA
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-82Y / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 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)29,1504
Polymers28,4052
Non-polymers7452
Water0
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5752
Polymers14,2021
Non-polymers3721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5752
Polymers14,2021
Non-polymers3721
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.139, 88.139, 98.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 14202.445 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 (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-82Y / N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide


Mass: 372.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16N2O5S

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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: 3.89 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.5 M ammonium sulfate in 100 mM TRIS (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.08 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.3→60.37 Å / Num. obs: 6991 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 28

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.3→60.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.15
RfactorNum. reflection% reflection
Rfree0.2957 367 5.25 %
Rwork0.276 --
obs0.279 6991 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→60.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 52 0 1923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031977
X-RAY DIFFRACTIONf_angle_d0.8782660
X-RAY DIFFRACTIONf_dihedral_angle_d14.176762
X-RAY DIFFRACTIONf_chiral_restr0.028264
X-RAY DIFFRACTIONf_plane_restr0.003341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3019-3.77560.31751190.30462150X-RAY DIFFRACTION95
3.7756-4.74120.27441130.27792155X-RAY DIFFRACTION95
4.7412-17.52750.29941350.25852247X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -8.6409 Å / Origin y: 35.0881 Å / Origin z: -5.6359 Å
111213212223313233
T0.7398 Å2-0.0748 Å20.0131 Å2-0.8473 Å20.1086 Å2--0.3123 Å2
L1.7746 °2-0.1959 °2-0.87 °2-3.0289 °20.3822 °2--0.448 °2
S-0.0092 Å °0.2293 Å °-0.1543 Å °-0.2149 Å °0.0996 Å °0.318 Å °0.1183 Å °-0.0828 Å °-0.1425 Å °
Refinement TLS groupSelection details: all

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