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- PDB-5hm0: Crystal structure of the first bromodomain of human BRD4 bound to... -

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Basic information

Entry
Database: PDB / ID: 5hm0
TitleCrystal structure of the first bromodomain of human BRD4 bound to benzoisoxazoloazepine 3
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / bromodomain
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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 I / Brdt, bromodomain, repeat II / 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 I / Brdt, bromodomain, repeat II / 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-62V / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.395 Å
AuthorsJayaram, H. / Poy, F. / Setser, J.W. / Bellon, S.F.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Identification of a Benzoisoxazoloazepine Inhibitor (CPI-0610) of the Bromodomain and Extra-Terminal (BET) Family as a Candidate for Human Clinical Trials.
Authors: Albrecht, B.K. / Gehling, V.S. / Hewitt, M.C. / Vaswani, R.G. / Cote, A. / Leblanc, Y. / Nasveschuk, C.G. / Bellon, S. / Bergeron, L. / Campbell, R. / Cantone, N. / Cooper, M.R. / Cummings, ...Authors: Albrecht, B.K. / Gehling, V.S. / Hewitt, M.C. / Vaswani, R.G. / Cote, A. / Leblanc, Y. / Nasveschuk, C.G. / Bellon, S. / Bergeron, L. / Campbell, R. / Cantone, N. / Cooper, M.R. / Cummings, R.T. / Jayaram, H. / Joshi, S. / Mertz, J.A. / Neiss, A. / Normant, E. / O'Meara, M. / Pardo, E. / Poy, F. / Sandy, P. / Supko, J. / Sims, R.J. / Harmange, J.C. / Taylor, A.M. / Audia, J.E.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4352
Polymers15,1261
Non-polymers3091
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.682, 47.722, 78.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15126.339 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-62V / 6-(4-chlorophenyl)-1-methyl-4H-[1,2]oxazolo[5,4-d][2]benzazepine


Mass: 308.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13ClN2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 3.4-3.8 M sodium formate, 0.1 M Tris pH 7.8, and 10% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.395→50 Å / Num. obs: 25403 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.6
Reflection shellResolution: 1.395→1.46 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.583 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.395→40.73 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.865 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.072 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22619 1292 5.1 %RANDOM
Rwork0.19024 ---
obs0.19205 24051 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.161 Å2
Baniso -1Baniso -2Baniso -3
1-5.34 Å2-0 Å20 Å2
2---3.39 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: 1 / Resolution: 1.395→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 22 112 1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021105
X-RAY DIFFRACTIONr_bond_other_d00.021048
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9941510
X-RAY DIFFRACTIONr_angle_other_deg0.7843.0032423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23525.76952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70415193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.652153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2582.022501
X-RAY DIFFRACTIONr_mcbond_other2.1522.016500
X-RAY DIFFRACTIONr_mcangle_it2.9153.021625
X-RAY DIFFRACTIONr_mcangle_other2.9323.028626
X-RAY DIFFRACTIONr_scbond_it3.9322.408604
X-RAY DIFFRACTIONr_scbond_other3.9292.408605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.683.454885
X-RAY DIFFRACTIONr_long_range_B_refined7.03118.2351379
X-RAY DIFFRACTIONr_long_range_B_other7.02818.2411380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.395→1.431 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 80 -
Rwork0.393 1390 -
obs--79.25 %
Refinement TLS params.Method: refined / Origin x: -10.584 Å / Origin y: -3.3051 Å / Origin z: 8.1865 Å
111213212223313233
T0.0235 Å20 Å20.0229 Å2-0.132 Å2-0.0059 Å2--0.069 Å2
L0.0911 °20.406 °2-0.1407 °2-2.2516 °2-0.4133 °2--0.4522 °2
S-0.0368 Å °-0.0331 Å °-0.0239 Å °-0.2202 Å °0.013 Å °-0.1542 Å °0.0222 Å °0.0393 Å °0.0238 Å °

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