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- PDB-9x7c: Crystal Structure of BRD2 BD1 domain in complex with small molecu... -

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Basic information

Entry
Database: PDB / ID: 9x7c
TitleCrystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Mivebresib ABBV-075
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / BRD2 / Cancer Ligand bound / Inhbitor
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / 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: 2.3 Å
AuthorsJwala, N. / Chandrasekhar, A. / NarasimhaRao, K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal Structure of BRD2 BD1 domain in complex with small molecule inhibitor Mivebresib ABBV-075
Authors: Jwala, N. / Chandrasekhar, A. / NarasimhaRao, K.
History
DepositionOct 16, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0976
Polymers38,7183
Non-polymers1,3783
Water1,22568
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7314
Polymers25,8122
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area11270 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7314
Polymers25,8122
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1920 Å2
ΔGint-11 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.700, 55.960, 69.330
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-613-

HOH

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Components

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


Mass: 12906.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Bromodomain BRD2BD1 domain / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 3 / Source method: obtained synthetically / Formula: C22H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1M Hepes (7.5), 26% PEG 3350, 0.2M Amm sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5678 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Oct 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5678 Å / Relative weight: 1
ReflectionResolution: 2.3→56.59 Å / Num. obs: 19465 / % possible obs: 99.9 % / Redundancy: 3.1 % / CC1/2: 0.972 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.39 Å / Rmerge(I) obs: 0.261 / Num. unique obs: 6059 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→56.59 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.779 / SU B: 8.673 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28403 947 4.9 %RANDOM
Rwork0.21157 ---
obs0.21513 18517 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.07 Å2
2---0.05 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.3→56.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 96 68 2849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122865
X-RAY DIFFRACTIONr_bond_other_d0.0020.0257
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.7083891
X-RAY DIFFRACTIONr_angle_other_deg2.3073117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.07959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42910507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0236
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_it1.7031.7061281
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7863.0491596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2511.8951584
X-RAY DIFFRACTIONr_scbond_other2.2511.8961585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6743.412296
X-RAY DIFFRACTIONr_long_range_B_refined13.37122.015233
X-RAY DIFFRACTIONr_long_range_B_other13.3721.895198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 66 -
Rwork0.293 1362 -
obs--99.86 %

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