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- PDB-4uiy: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(1,1-dioxo-1-thian-4-... -

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Basic information

Entry
Database: PDB / ID: 4uiy
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(1,1-dioxo-1-thian-4-yl)- 5-methyl-4-oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c- pyridine-2-carboximidamide
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4BRD4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
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 / 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-5V2 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChung, C. / Theodoulou, N.T. / Bamborough, P. / Humphreys, P.G.
CitationJournal: J.Med.Chem. / Year: 2016
Title: The Discovery of I-Brd9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition.
Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / ...Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Michon, A. / Molnar, J. / Robson, S.C. / Tomkinson, N.C.O. / Kouzarides, T. / Prinjha, R.K. / Humphreys, P.G.
History
DepositionApr 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type

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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)15,7695
Polymers15,0991
Non-polymers6704
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.350, 44.240, 78.640
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 / BRD4 / PROTEIN HUNK1 / HUMAN BRD4


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5V2 / N-[1,1-bis(oxidanylidene)thian-4-yl]-5-methyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide


Mass: 483.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20F3N3O3S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.15 Å3/Da / Density % sol: 42.83 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% PEG3350, 0.2M KSCN, 0.1M BTP PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→39.32 Å / Num. obs: 31523 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.1 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→39.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.393 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 1587 5 %RANDOM
Rwork0.15643 ---
obs0.15781 29935 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 44 264 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191185
X-RAY DIFFRACTIONr_bond_other_d0.0010.02809
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9371623
X-RAY DIFFRACTIONr_angle_other_deg0.94331984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0155130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4632655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.773153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.070.0211267
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02218
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 89 -
Rwork0.2 1696 -
obs--76.84 %
Refinement TLS params.Method: refined / Origin x: 25.5943 Å / Origin y: 40.655 Å / Origin z: 8.9448 Å
111213212223313233
T0.0163 Å20.0044 Å2-0.0031 Å2-0.009 Å2-0.0008 Å2--0.0106 Å2
L0.0475 °20.1324 °2-0.0457 °2-0.3829 °2-0.1323 °2--0.2511 °2
S-0.0044 Å °0.0067 Å °-0.0013 Å °-0.0009 Å °0.027 Å °-0.0095 Å °0.0347 Å °-0.0254 Å °-0.0226 Å °

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