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- PDB-7c6p: Bromodomain-containing 4 BD2 in complex with 3',4',7,8- Tetrahydr... -

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Basic information

Entry
Database: PDB / ID: 7c6p
TitleBromodomain-containing 4 BD2 in complex with 3',4',7,8- Tetrahydroxyflavonoid
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / BRD4 / BD2 / 3' / 4' / 7 / 8- tetrahydroxyflavonoid / Acute myeloid leukemia / c-MYC
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, conserved site / Bromodomain signature. ...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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-SQH / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsLi, J. / Yu, K. / Luo, Y. / Zheng, W. / Liang, W. / Zhu, J.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2021
Title: Discovery of the natural product 3',4',7,8-tetrahydroxyflavone as a novel and potent selective BRD4 bromodomain 2 inhibitor.
Authors: Li, J. / Zou, W. / Yu, K. / Liu, B. / Liang, W. / Wang, L. / Lu, Y. / Jiang, Z. / Wang, A. / Zhu, J.
History
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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)13,0932
Polymers12,8071
Non-polymers2861
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.590, 63.010, 70.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

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Components

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


Mass: 12806.933 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-SQH / 2-[3,4-bis(oxidanyl)phenyl]-7,8-bis(oxidanyl)chromen-4-one / 3',4',7,8-Tetrahydroxyflavone


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 2. 20 % v/v Polyethylene glycol monomethyl ether 2000, 100 mM Tris PH8.5, 200 mM Trimethylamine N-oxide, 295K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.73→35.25 Å / Num. obs: 16261 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 24.36 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.3
Reflection shellResolution: 1.73→8.99 Å / Num. unique obs: 16261 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.14_3235refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UEP

5uep


Resolution: 1.73→35.25 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 1619 10 %
Rwork0.1888 14566 -
obs0.1921 16185 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.25 Å2 / Biso mean: 31.8021 Å2 / Biso min: 15.86 Å2
Refinement stepCycle: final / Resolution: 1.73→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 21 137 1010
Biso mean--28.28 42.34 -
Num. residues----105
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7301-1.7810.30681330.31188100
1.781-1.83840.29651300.27621183100
1.8384-1.90420.31061330.25691199100
1.9042-1.98040.32951350.24531208100
1.9804-2.07050.28081310.21391185100
2.0705-2.17970.22831330.19331196100
2.1797-2.31620.25081350.1831120499
2.3162-2.4950.241330.17491204100
2.495-2.7460.22411370.1811227100
2.746-3.14310.19321370.19021231100
3.1431-3.95910.18591360.1705123499
3.9591-35.250.19881460.1686130799
Refinement TLS params.Method: refined / Origin x: -2.4128 Å / Origin y: -20.5929 Å / Origin z: -0.5109 Å
111213212223313233
T0.1663 Å20.0271 Å20.0035 Å2-0.1966 Å20.0112 Å2--0.1793 Å2
L2.0885 °20.073 °20.0749 °2-1.529 °20.1748 °2--2.5575 °2
S-0.0133 Å °-0.0041 Å °0.0188 Å °-0.0317 Å °0.0568 Å °0.1112 Å °-0.0451 Å °-0.2093 Å °-0.0467 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA353 - 501
2X-RAY DIFFRACTION1allS1 - 145

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