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- PDB-6x7d: BRD4 Bromodomain 1 in complex with multi-action inhibitor SF2523P -

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Basic information

Entry
Database: PDB / ID: 6x7d
TitleBRD4 Bromodomain 1 in complex with multi-action inhibitor SF2523P
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / BRD4 / PI3K
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-UT4 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVann, K.R. / Kutateladze, T.G.
CitationJournal: Sci Rep / Year: 2020
Title: Design of thienopyranone-based BET inhibitors that bind multiple synthetic lethality targets.
Authors: Vann, K.R. / Pal, D. / Morales, G.A. / Burgoyne, A.M. / Durden, D.L. / Kutateladze, T.G.
History
DepositionMay 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2754
Polymers31,5342
Non-polymers7412
Water2,090116
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1382
Polymers15,7671
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1382
Polymers15,7671
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.147, 39.832, 62.035
Angle α, β, γ (deg.)90.000, 106.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15767.175 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-UT4 / 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one


Mass: 370.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.5 M Ammonium Sulfate and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8982 / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Rrim(I) all: 0.117 / Χ2: 1.478 / Net I/σ(I): 8 / Num. measured all: 29239
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.10.3498930.9080.2140.4131.10797.4
2.59-2.693.20.3158920.920.1890.3711.10695.6
2.69-2.823.30.249150.9570.1450.2831.12697.7
2.82-2.963.30.1828990.9750.1060.2131.21496.7
2.96-3.153.40.1519110.980.0890.1771.22198
3.15-3.393.30.1089020.9880.0640.1271.48597
3.39-3.733.40.0859000.9870.0510.11.66595.6
3.73-4.273.30.0738790.9910.0450.0861.81993.5
4.27-5.383.10.0728710.990.0460.0861.90791.6
5.38-5030.0689200.9920.0420.082.24792.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mxf

3mxf


Resolution: 2.5→35.262 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 859 10.09 %
Rwork0.1946 7658 -
obs0.2018 8517 91.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.44 Å2 / Biso mean: 38.4021 Å2 / Biso min: 21.92 Å2
Refinement stepCycle: final / Resolution: 2.5→35.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 52 116 2277
Biso mean--35.28 35.72 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5002-2.65680.37941350.2606120687
2.6568-2.86180.32961370.2391122789
2.8618-3.14970.31031470.2307128793
3.1497-3.6050.27741470.1952131895
3.605-4.54050.2431460.1541129993
4.5405-35.260.20731470.1812132191

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