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- PDB-32pp: CRYSTAL STRUCTURE OF BRD4 BD1 IN COMPLEX WITH Compound 9 -

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Basic information

Entry
Database: PDB / ID: 32pp
TitleCRYSTAL STRUCTURE OF BRD4 BD1 IN COMPLEX WITH Compound 9
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / VIENNA / Bromodomain
Function / homology
Function and homology information


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / Regulation of PD-L1(CD274) transcription / regulation of inflammatory response / chromosome / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / 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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsBader, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Med Chem / Year: 2024
Title: Probing Protein-Ligand Methyl-pi Interaction Geometries through Chemical Shift Measurements of Selectively Labeled Methyl Groups.
Authors: Beier, A. / Platzer, G. / Hofurthner, T. / Ptaszek, A.L. / Lichtenecker, R.J. / Geist, L. / Fuchs, J.E. / McConnell, D.B. / Mayer, M. / Konrat, R.
History
DepositionJul 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4924
Polymers15,0991
Non-polymers3923
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint5 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.349, 78.749, 31.850
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
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-A1KEP / ~{N},3,8-trimethyl-~{N}-(pyridin-2-ylmethyl)-[1,2,4]triazolo[4,3-b]pyridazin-6-amine


Mass: 268.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 19 % PEG 3350, 0.2 M Sodium Malonate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.44→40.58 Å / Num. obs: 13973 / % possible obs: 64 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.36 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.9
Reflection shellResolution: 1.44→1.595 Å / Num. unique obs: 699 / CC1/2: 0.585

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→17.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.237 715 5.12 %RANDOM
Rwork0.209 ---
obs0.21 13952 62.7 %-
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.3586 Å20 Å20 Å2
2---4.3641 Å20 Å2
3---6.7227 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.44→17.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 28 63 1134
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081108HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.881506HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d380SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes184HARMONIC5
X-RAY DIFFRACTIONt_it1108HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion17.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion139SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1415SEMIHARMONIC4
LS refinement shellResolution: 1.44→1.55 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.1933 -3.7 %
Rwork0.214 390 -
all0.2133 405 -
obs--9.06 %
Refinement TLS params.Method: refined / Origin x: -3.0405 Å / Origin y: 8.4828 Å / Origin z: -9.5257 Å
111213212223313233
T-0.0565 Å2-0.0058 Å2-0.0047 Å2--0.0861 Å20.0147 Å2--0.0805 Å2
L0.8914 °2-0.1125 °2-0.0581 °2-0.4475 °2-0.067 °2--0.205 °2
S0.022 Å °-0.04 Å °-0.0644 Å °0.008 Å °0.0013 Å °0.0777 Å °0.0089 Å °0.0192 Å °-0.0234 Å °
Refinement TLS groupSelection details: { A|* }

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