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- PDB-6jjb: BRD4 in complex with ZZM1 -

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Basic information

Entry
Database: PDB / ID: 6jjb
TitleBRD4 in complex with ZZM1
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN/INHIBITOR / BRD4 / Inhibitor / SIGNALING PROTEIN-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 / chromatin / 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-BT0 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.508 Å
AuthorsXu, J. / Chen, Y. / Jiang, F. / Zhu, J.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Benzo[cd]indol-2(1H)-ones and Pyrrolo[4,3,2-de]quinolin-2(1H)-ones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain with ...Title: Discovery of Benzo[cd]indol-2(1H)-ones and Pyrrolo[4,3,2-de]quinolin-2(1H)-ones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain with Potential High Efficiency against Acute Gouty Arthritis.
Authors: Jiang, F. / Hu, Q. / Zhang, Z. / Li, H. / Li, H. / Zhang, D. / Li, H. / Ma, Y. / Xu, J. / Chen, H. / Cui, Y. / Zhi, Y. / Zhang, Y. / Xu, J. / Zhu, J. / Lu, T. / Chen, Y.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2522
Polymers14,8831
Non-polymers3681
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7510 Å2
Unit cell
Length a, b, c (Å)32.480, 47.070, 78.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14883.188 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 BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-BT0 / 2-methoxy-N-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)benzenesulfonamide


Mass: 368.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 4.0M HCOONa

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.508→26.73 Å / Num. obs: 19301 / % possible obs: 95.41 % / Redundancy: 33.3 % / Net I/σ(I): 116.02
Reflection shellResolution: 1.508→1.562 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3235refinement
PDB_EXTRACT3.24data extraction
TRUNCATEdata reduction
PHASERphasing
RefinementResolution: 1.508→26.73 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2278 1880 10.01 %
Rwork0.194 --
obs0.1974 18772 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.25 Å2 / Biso mean: 23.7981 Å2 / Biso min: 10.5 Å2
Refinement stepCycle: final / Resolution: 1.508→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 26 119 1191
Biso mean--50.85 32.88 -
Num. residues----125
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.508-1.54880.35131390.2933123192
1.5488-1.59440.36181390.2668125395
1.5944-1.64580.28771400.2566126095
1.6458-1.70460.32871450.2379129796
1.7046-1.77290.27961430.2284129097
1.7729-1.85350.26071470.218132298
1.8535-1.95130.28141470.2024132198
1.9513-2.07350.22171460.1895132597
2.0735-2.23350.20981470.1822131597
2.2335-2.45820.22341440.1829129595
2.4582-2.81370.22621430.1912128194
2.8137-3.5440.19581470.1741133795
3.544-26.730.19131530.1752136592
Refinement TLS params.Method: refined / Origin x: 22.867 Å / Origin y: 20.229 Å / Origin z: 47.811 Å
111213212223313233
T0.2284 Å2-0.0083 Å20.0266 Å2-0.145 Å2-0.012 Å2--0.1224 Å2
L0.5676 °20.184 °2-0.2217 °2-0.8451 °2-0.0117 °2--0.6674 °2
S-0.0109 Å °0.0345 Å °0.0197 Å °-0.1495 Å °0.0379 Å °-0.0547 Å °0.0237 Å °-0.0143 Å °-0.0158 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 43:167 OR RESID 201:201 OR RESID 301:419 ) )A43 - 167
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 43:167 OR RESID 201:201 OR RESID 301:419 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 43:167 OR RESID 201:201 OR RESID 301:419 ) )A301 - 419

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