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- PDB-4bw4: The first bromodomain of human BRD4 in complex with 3,5 dimethyli... -

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Basic information

Entry
Database: PDB / ID: 4bw4
TitleThe first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / 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 / 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-9B6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsChung, C. / Mirguet, O. / Lamotte, Y. / Bamborough, P. / Delannee, D. / Bouillot, A. / Gellibert, F. / Krysa, G. / Lewis, A. / Witherington, J. ...Chung, C. / Mirguet, O. / Lamotte, Y. / Bamborough, P. / Delannee, D. / Bouillot, A. / Gellibert, F. / Krysa, G. / Lewis, A. / Witherington, J. / Huet, P. / Dudit, Y. / Trottet, L. / Nicodeme, E.
CitationJournal: Chemmedchem / Year: 2014
Title: Naphthyridines as Novel Bet Family Bromodomain Inhibitors.
Authors: Mirguet, O. / Lamotte, Y. / Chung, C. / Bamborough, P. / Delannee, D. / Bouillot, A. / Gellibert, F. / Krysa, G. / Lewis, A. / Witherington, J. / Huet, P. / Dudit, Y. / Trottet, L. / Nicodeme, E.
History
DepositionJun 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)15,5712
Polymers15,0991
Non-polymers4711
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.670, 48.665, 60.880
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


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-9B6 / 7-(3,5-dimethylisoxazol-4-yl)-8-methoxy-1-(2-(trifluoromethoxy)phenyl)-1h-imidazo[4,5-c][1,5]naphthyridin-2(3h)-one


Mass: 471.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16F3N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.14 Å3/Da / Density % sol: 42.58 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS PH8.0, 25% PE6000, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU A200 / Date: Jan 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.67→60.88 Å / Num. obs: 15303 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→32.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.1 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21955 758 5 %RANDOM
Rwork0.18874 ---
obs0.19019 14442 97.98 %-
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: 20.085 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.67→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 34 231 1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191150
X-RAY DIFFRACTIONr_bond_other_d0.0010.021078
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9751577
X-RAY DIFFRACTIONr_angle_other_deg0.73932496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6715134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7152655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2915203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.815153
X-RAY DIFFRACTIONr_chiral_restr0.0580.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
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: 1.674→1.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 55 -
Rwork0.244 1015 -
obs--95.28 %
Refinement TLS params.Method: refined / Origin x: 3.793 Å / Origin y: 5.1103 Å / Origin z: 19.8294 Å
111213212223313233
T0.0111 Å20.0042 Å2-0.0076 Å2-0.0117 Å2-0.0104 Å2--0.0173 Å2
L0.5777 °2-0.2703 °2-0.3881 °2-0.5139 °20.5989 °2--0.9945 °2
S-0.0444 Å °0.0039 Å °-0.0334 Å °-0.0239 Å °-0.0121 Å °0.0693 Å °0.0048 Å °-0.0068 Å °0.0565 Å °

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