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- PDB-5cfw: Selective pharmacological inhibition of the CREB binding protein ... -

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Basic information

Entry
Database: PDB / ID: 5cfw
TitleSelective pharmacological inhibition of the CREB binding protein bromodomain regulates inflammatory cytokines in macrophages and RGS4 in neurons
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION/INHIBITOR / inhibitor complex / TRANSCRIPTION-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-53W / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsChekler, E.L. / Jones, L.H.
CitationJournal: Chem.Biol. / Year: 2015
Title: Transcriptional Profiling of a Selective CREB Binding Protein Bromodomain Inhibitor Highlights Therapeutic Opportunities.
Authors: Chekler, E.L. / Pellegrino, J.A. / Lanz, T.A. / Denny, R.A. / Flick, A.C. / Coe, J. / Langille, J. / Basak, A. / Liu, S. / Stock, I.A. / Sahasrabudhe, P. / Bonin, P.D. / Lee, K. / Pletcher, M.T. / Jones, L.H.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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 / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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)15,5602
Polymers15,0991
Non-polymers4611
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.610, 50.270, 57.210
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: 15099.380 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168
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-53W / 5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[2-(4-methoxyphenyl)ethyl]-1-[2-(morpholin-4-yl)ethyl]-1H-benzimidazole


Mass: 460.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.89 Å3/Da / Density % sol: 34.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.15→31.11 Å / Num. obs: 37951 / % possible obs: 92.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 13.64 Å2 / Rmerge F obs: 0.033 / Rmerge(I) obs: 0.033 / Net I/σ(I): 21.1
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.4 / % possible all: 55.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.15→13.76 Å / Cor.coef. Fo:Fc: 0.9662 / Cor.coef. Fo:Fc free: 0.9569 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.046 / SU Rfree Blow DPI: 0.048 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1894 4.99 %RANDOM
Rwork0.1857 ---
obs0.1868 37922 91.85 %-
Displacement parametersBiso mean: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.8083 Å20 Å20 Å2
2--0.3172 Å20 Å2
3---0.4911 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.15→13.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 34 176 1275
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011167HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981621HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d401SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes187HARMONIC5
X-RAY DIFFRACTIONt_it1167HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion16.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion140SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1479SEMIHARMONIC4
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.244 74 4.35 %
Rwork0.2178 1627 -
all0.219 1701 -
obs--91.85 %
Refinement TLS params.Method: refined / Origin x: 6.5084 Å / Origin y: -9.3262 Å / Origin z: -16.545 Å
111213212223313233
T-0.0165 Å20.0017 Å2-0.0012 Å2--0.0305 Å2-0.0203 Å2---0.0228 Å2
L1.18 °2-0.4827 °20.5552 °2-0.652 °2-0.3886 °2--0.8787 °2
S-0.1081 Å °-0.129 Å °0.1009 Å °0.0563 Å °0.0456 Å °-0.0302 Å °-0.0242 Å °-0.073 Å °0.0625 Å °
Refinement TLS groupSelection details: { A|* }

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