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- PDB-5i88: BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dih... -

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Basic information

Entry
Database: PDB / ID: 5i88
TitleBRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / BRD4 / bromodomain / epigenetics / structure-based design
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 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / 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-69G / TRIETHYLENE GLYCOL / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMurray, J.M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.
Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / ...Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / Kiefer, J.R. / Jiang, Y. / Murray, J. / Nasveschuk, C.G. / Pardo, E. / Poy, F. / Romero, F.A. / Tang, Y. / Wang, J. / Xu, Z. / Zawadzke, L.E. / Zhu, X. / Albrecht, B.K. / Magnuson, S.R. / Bellon, S. / Cochran, A.G.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)15,7207
Polymers14,9401
Non-polymers7806
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint8 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.176, 48.561, 60.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 14940.172 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

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Non-polymers , 6 types, 136 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-69G / 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide


Mass: 335.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 20% ethylene glycol, 0.1 M Bis-Tris pH 6.8, 20% polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 25580 / % possible obs: 97.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.13 Å2 / Rmerge(I) obs: 0.065 / Net I/av σ(I): 31.488 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.456.80.974195.1
1.45-1.517.20.703196.4
1.51-1.587.40.494196.5
1.58-1.667.30.346197.6
1.66-1.767.30.236197
1.76-1.97.30.149198.2
1.9-2.097.30.094198.2
2.09-2.397.20.074198.7
2.39-3.0270.06199
3.02-506.70.04197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→35.615 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.96
RfactorNum. reflection% reflection
Rfree0.2022 1274 5 %
Rwork0.1486 --
obs0.1513 25497 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.39 Å2 / Biso mean: 25.2773 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 1.4→35.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 64 130 1245
Biso mean--36 39.76 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051174
X-RAY DIFFRACTIONf_angle_d0.7571590
X-RAY DIFFRACTIONf_chiral_restr0.069164
X-RAY DIFFRACTIONf_plane_restr0.005204
X-RAY DIFFRACTIONf_dihedral_angle_d17.025461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4560.28181260.21842592271895
1.456-1.52230.22991500.18632619276996
1.5223-1.60260.22051440.1582632277697
1.6026-1.7030.20191350.13332642277797
1.703-1.83450.17811550.12772660281598
1.8345-2.0190.17871230.12992725284898
2.019-2.31120.20631270.13482746287399
2.3112-2.91160.19511520.15232758291099
2.9116-35.6270.2051620.15262849301198

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