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- PDB-24os: Crystal Structure of BRD3 BD1 domain in complex with small molecu... -

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Basic information

Entry
Database: PDB / ID: 24os
TitleCrystal Structure of BRD3 BD1 domain in complex with small molecule inhibitor IBET-762
ComponentsBromodomain-containing protein 3
KeywordsTRANSCRIPTION / BRD3 / Cancer Ligand bound / Inhibitor
Function / homology
Function and homology information


histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K27cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / histone reader activity / protein localization to chromatin / molecular condensate scaffold activity / histone binding ...histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K27cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / histone reader activity / protein localization to chromatin / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
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 ...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
Chem-EAM / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJwala, N. / Chandrasekhar, A. / NarasimhaRao, K.
Funding support India, 1items
OrganizationGrant numberCountry
Other private India
CitationJournal: To Be Published
Title: Crystal Structure of BRD3 BD1 domain in complex with small molecule inhibitor IBET-762
Authors: Jwala, N. / Chandrasekhar, A. / NarasimhaRao, K.
History
DepositionMar 13, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7634
Polymers28,9152
Non-polymers8482
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.171, 55.355, 122.334
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 3 / RING3-like protein


Mass: 14457.729 Da / Num. of mol.: 2 / Fragment: BD1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pET21a-BRD3BD1 (24-144) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: Q15059
#2: Chemical ChemComp-EAM / 2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide


Mass: 423.895 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10mM HEPES (pH 7.5),150mM NaCl, 0.5mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.83→43.17 Å / Num. obs: 26527 / % possible obs: 99 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 1.063 / Num. unique obs: 1357 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→41.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.876 / SU B: 5.398 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31446 1294 4.9 %RANDOM
Rwork0.24896 ---
obs0.25226 25173 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.83→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 60 110 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122131
X-RAY DIFFRACTIONr_bond_other_d0.0020.0244
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6992892
X-RAY DIFFRACTIONr_angle_other_deg0.801394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8435240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.0154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58610379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0218
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_it2.4753.146966
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7525.6271204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5213.3951165
X-RAY DIFFRACTIONr_scbond_other3.5153.3961164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3126.0731689
X-RAY DIFFRACTIONr_long_range_B_refined19.88237.44022
X-RAY DIFFRACTIONr_long_range_B_other19.81936.713953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.875 Å
RfactorNum. reflection% reflection
Rfree0.365 74 -
Rwork0.362 1607 -
obs--86.83 %

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