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- PDB-5lj1: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 8-(((3R,4R,5S)-3-((4,4-... -

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Basic information

Entry
Database: PDB / ID: 5lj1
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
ComponentsBromodomain-containing protein 4
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 / 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-6XX / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChung, C. / Bamborough, P. / Demont, E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: A Chemical Probe for the ATAD2 Bromodomain.
Authors: Bamborough, P. / Chung, C.W. / Demont, E.H. / Furze, R.C. / Bannister, A.J. / Che, K.H. / Diallo, H. / Douault, C. / Grandi, P. / Kouzarides, T. / Michon, A.M. / Mitchell, D.J. / Prinjha, R. ...Authors: Bamborough, P. / Chung, C.W. / Demont, E.H. / Furze, R.C. / Bannister, A.J. / Che, K.H. / Diallo, H. / Douault, C. / Grandi, P. / Kouzarides, T. / Michon, A.M. / Mitchell, D.J. / Prinjha, R.K. / Rau, C. / Robson, S. / Sheppard, R.J. / Upton, R. / Watson, R.J.
History
DepositionJul 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,6893
Polymers15,0991
Non-polymers5902
Water2,954164
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.670, 109.190, 30.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15099.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SM residues residual after cleavage of expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-6XX / 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one


Mass: 527.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35F2N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2NaNO3, 20% PEG3350 at 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→41.67 Å / Num. obs: 11147 / % possible obs: 98.1 % / Redundancy: 4.3 % / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.67 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.67 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23699 532 4.8 %RANDOM
Rwork0.16794 ---
obs0.17108 10604 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.87 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 42 164 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021081
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9661549
X-RAY DIFFRACTIONr_angle_other_deg0.76532502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9875126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24525.92654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57415197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.655153
X-RAY DIFFRACTIONr_chiral_restr0.0670.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211247
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_it2.6544.086507
X-RAY DIFFRACTIONr_mcbond_other2.6554.068506
X-RAY DIFFRACTIONr_mcangle_it3.9369.114632
X-RAY DIFFRACTIONr_mcangle_other3.9349.146633
X-RAY DIFFRACTIONr_scbond_it3.4364.758629
X-RAY DIFFRACTIONr_scbond_other3.4364.758629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.58610.39918
X-RAY DIFFRACTIONr_long_range_B_refined8.05519.8491482
X-RAY DIFFRACTIONr_long_range_B_other8.05519.8491482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 30 -
Rwork0.226 773 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: -14.812 Å / Origin y: -14.927 Å / Origin z: 13.064 Å
111213212223313233
T0.1059 Å20.0542 Å20.0476 Å2-0.0455 Å20.0307 Å2--0.0525 Å2
L0.5308 °2-0.5065 °20.2746 °2-2.7404 °2-1.3185 °2--0.6421 °2
S-0.1962 Å °-0.0517 Å °-0.0441 Å °0.2024 Å °0.1481 Å °-0.1429 Å °-0.1223 Å °-0.088 Å °0.0481 Å °

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