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- PDB-32sb: CRYSTAL STRUCTURE OF BRD4-BD1 IN COMPLEX WITH COMPOUND 16 -

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Basic information

Entry
Database: PDB / ID: 32sb
TitleCRYSTAL STRUCTURE OF BRD4-BD1 IN COMPLEX WITH COMPOUND 16
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Bromodomain / Inhibitor
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 / MOLECULAR REPLACEMENT / Resolution: 1.81 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 22, 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)15,3612
Polymers15,0991
Non-polymers2611
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.779, 44.596, 78.647
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-A1KEX / (7~{R})-2-azanyl-8-cyclopentyl-5,7-dimethyl-7~{H}-pteridin-6-one


Mass: 261.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 % ethylene glycol, 0.1 M sodium nitrate, 18 %PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.81→26.69 Å / Num. obs: 11961 / % possible obs: 96.8 % / Redundancy: 6 % / Biso Wilson estimate: 17.17 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Net I/σ(I): 19.3 / Num. measured all: 71256
Reflection shellResolution: 1.81→1.91 Å / % possible obs: 79.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.411 / Num. measured all: 4035 / Num. unique obs: 1399 / Rpim(I) all: 0.283 / Rrim(I) all: 0.503 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→26.69 Å / Cor.coef. Fo:Fc: 0.9303 / Cor.coef. Fo:Fc free: 0.9187 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 596 5 %RANDOM
Rwork0.2014 ---
obs0.2031 11913 96.72 %-
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.7636 Å20 Å2
3----0.1135 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 1.81→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 19 148 1242
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081127HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.911539HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d397SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes160HARMONIC5
X-RAY DIFFRACTIONt_it1127HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion15.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion142SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1457SEMIHARMONIC4
LS refinement shellResolution: 1.81→1.98 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3174 128 5.19 %
Rwork0.2336 2339 -
all0.2376 2467 -
obs--96.72 %
Refinement TLS params.Method: refined / Origin x: 11.7983 Å / Origin y: 3.5184 Å / Origin z: 8.8473 Å
111213212223313233
T-0.0188 Å2-0.0011 Å2-0.006 Å2--0.0355 Å20.0195 Å2---0.0454 Å2
L0.6213 °20.1248 °20.3422 °2-1.2351 °20.3448 °2--1.2478 °2
S-0.0091 Å °0.0337 Å °-0.0055 Å °0.0093 Å °0.04 Å °0.0077 Å °-0.0614 Å °0.0294 Å °-0.0309 Å °
Refinement TLS groupSelection details: { A|* }

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