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- PDB-5ueu: BRD4_BD2_A-1107604 -

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Basic information

Entry
Database: PDB / ID: 5ueu
TitleBRD4_BD2_A-1107604
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN/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 / 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 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-0S6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPark, C.H.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Fragment-Based, Structure-Enabled Discovery of Novel Pyridones and Pyridone Macrocycles as Potent Bromodomain and Extra-Terminal Domain (BET) Family Bromodomain Inhibitors.
Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, ...Authors: Wang, L. / Pratt, J.K. / Soltwedel, T. / Sheppard, G.S. / Fidanze, S.D. / Liu, D. / Hasvold, L.A. / Mantei, R.A. / Holms, J.H. / McClellan, W.J. / Wendt, M.D. / Wada, C. / Frey, R. / Hansen, T.M. / Hubbard, R. / Park, C.H. / Li, L. / Magoc, T.J. / Albert, D.H. / Lin, X. / Warder, S.E. / Kovar, P. / Huang, X. / Wilcox, D. / Wang, R. / Rajaraman, G. / Petros, A.M. / Hutchins, C.W. / Panchal, S.C. / Sun, C. / Elmore, S.W. / Shen, Y. / Kati, W.M. / McDaniel, K.F.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4444
Polymers25,6142
Non-polymers8302
Water4,053225
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2222
Polymers12,8071
Non-polymers4151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2222
Polymers12,8071
Non-polymers4151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.826, 64.544, 75.287
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: 12806.933 Da / Num. of mol.: 2 / Fragment: residues 352-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O60885
#2: Chemical ChemComp-0S6 / methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate


Mass: 414.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19ClN4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→75.3 Å / Num. obs: 13221 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 43.78 Å2 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
XDS2.11.7data reduction
SCALAdata scaling
Cootmodel building
BUSTER2.11.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo BRD4_BD2

Resolution: 2.26→42.22 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / Rfactor Rfree error: 0.02 / SU R Cruickshank DPI: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.221 651 4.92 %RANDOM
Rwork0.187 ---
obs0.189 13240 99.9 %-
Displacement parametersBiso mean: 42.11 Å2
Baniso -1Baniso -2Baniso -3
1--16.7935 Å20 Å20 Å2
2--4.6907 Å20 Å2
3---12.1028 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.26→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 56 223 2063
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081936HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.922634HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d666SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes291HARMONIC5
X-RAY DIFFRACTIONt_it1936HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion17.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
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_contact2343SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.227 162 6.1 %
Rwork0.208 2495 -
all0.209 2657 -
obs--99.33 %

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