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- PDB-9lkr: Crystal Structure of the bromodomain of human BRD9 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9lkr
TitleCrystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22076
ComponentsBromodomain-containing protein 9
KeywordsPROTEIN BINDING / BRD9 / Bromodomain
Function / homology
Function and homology information


GBAF complex / Formation of the non-canonical BAF (ncBAF) complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / histone reader activity / double-strand break repair via homologous recombination / site of double-strand break / nucleic acid binding / protein-macromolecule adaptor activity ...GBAF complex / Formation of the non-canonical BAF (ncBAF) complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / histone reader activity / double-strand break repair via homologous recombination / site of double-strand break / nucleic acid binding / protein-macromolecule adaptor activity / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsChen, Z. / Zhang, C. / Xu, H. / Wu, X. / Zhang, Y. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173745 China
CitationJournal: Acta Pharm Sin B / Year: 2025
Title: Key imidazolyl groups that induce phenylalanine flipping enhance the efficacy of oral BRD9 inhibitors for AML treatment.
Authors: Chen, Z. / Zhang, C. / Shen, H. / Xu, H. / Huang, Y. / Dong, R. / Tang, X. / Chai, S. / Li, J. / Xu, J. / Zhang, X. / Zhang, Y. / Wu, X. / Xu, Y.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7746
Polymers34,8672
Non-polymers9074
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.910, 68.370, 144.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 17433.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BRD9_HUMAN, Q9H8M2, sequence from 111-133 and 240-259 are tags. MKKGHHHHHHENLYFQGGSLKLS(M111-S133) ERLLALKRSMSFMQDMDFSQ(E240-Q259)
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-A1EKN / 1-[1-[4-(imidazol-1-ylmethyl)-3,5-dimethoxy-phenyl]indolizin-3-yl]ethanone


Mass: 375.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.28→72.25 Å / Num. obs: 38973 / % possible obs: 99.7 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Net I/σ(I): 19.9
Reflection shellResolution: 1.28→1.3 Å / % possible obs: 95.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.412 / Num. measured all: 8067 / Num. unique obs: 1794 / CC1/2: 0.878 / Rpim(I) all: 0.214 / Rrim(I) all: 0.467 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→72.25 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / SU B: 17.03 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R: 0.79 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32772 457 5.1 %RANDOM
Rwork0.25299 ---
obs0.25691 8477 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.861 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å2-0 Å2
2---2.67 Å20 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.68→72.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 0 64 0 1780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131828
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171742
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.7082454
X-RAY DIFFRACTIONr_angle_other_deg1.191.6214034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7822.32686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47415334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.153158
X-RAY DIFFRACTIONr_chiral_restr0.0620.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
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_it7.4138.059838
X-RAY DIFFRACTIONr_mcbond_other7.4168.053837
X-RAY DIFFRACTIONr_mcangle_it10.69712.0971044
X-RAY DIFFRACTIONr_mcangle_other10.69212.1041045
X-RAY DIFFRACTIONr_scbond_it6.9298.223990
X-RAY DIFFRACTIONr_scbond_other6.9278.223991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.87612.1181411
X-RAY DIFFRACTIONr_long_range_B_refined15.3127092
X-RAY DIFFRACTIONr_long_range_B_other15.3117093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3248 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.68→2.746 Å
RfactorNum. reflection% reflection
Rfree0.336 28 -
Rwork0.33 634 -
obs--100 %

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