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- PDB-9l61: Crystal Structure of BRD2 BD2 domain in complex with small molecu... -

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Basic information

Entry
Database: PDB / ID: 9l61
TitleCrystal Structure of BRD2 BD2 domain in complex with small molecule inhibitor Mivebresib ABBV-075
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / Bromodomain / Inhibitor / Small molecule / Drug discovery
Function / homology
Function and homology information


histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / histone H4K5ac reader activity / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / histone H4K5ac reader activity / histone H4K12ac reader activity / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / histone binding / spermatogenesis / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
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-8NG / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJwala, N. / Vijayshankar, N. / Thomas, A. / NarasimhaRao, K.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Crystal Structure of BRD2 BD2 domain in complex with small molecule inhibitor Mivebresib ABBV-075
Authors: Jwala, N. / NarasimhaRao, K.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2025Provider: 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 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9774
Polymers30,0582
Non-polymers9192
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.370, 41.630, 45.390
Angle α, β, γ (deg.)97.04, 112.86, 105.48
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1


Mass: 15029.115 Da / Num. of mol.: 2 / Fragment: BD2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: E.coli / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: P25440
#2: Chemical ChemComp-8NG / N-[4-(2,4-difluorophenoxy)-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)phenyl]ethanesulfonamide


Mass: 459.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis tris (5.5), 25% PEG 3350, 0.2M Sod chloride

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.21→40.44 Å / Num. obs: 9598 / % possible obs: 86.6 % / Redundancy: 2.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.6
Reflection shellResolution: 2.21→2.29 Å / Rmerge(I) obs: 0.157 / Num. unique obs: 527 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→40.44 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.783 / SU B: 12.542 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3038 390 5 %RANDOM
Rwork0.20839 ---
obs0.21314 7339 88.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.744 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.02 Å2-0.07 Å2
2--0.09 Å2-0.08 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 64 152 2044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121950
X-RAY DIFFRACTIONr_bond_other_d0.0030.0238
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.7192636
X-RAY DIFFRACTIONr_angle_other_deg2.364378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.84512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01710332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021504
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0224
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_it1.6511.99886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7323.5631104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3162.3981064
X-RAY DIFFRACTIONr_scbond_other2.3142.3981064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7474.2851533
X-RAY DIFFRACTIONr_long_range_B_refined11.03125.823473
X-RAY DIFFRACTIONr_long_range_B_other10.96625.813461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 32 -
Rwork0.242 520 -
obs--87.48 %

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