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- PDB-9km1: Crystal Structure of the bromodomain of human BRD9 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9km1
TitleCrystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22077
ComponentsBromodomain-containing protein 9
KeywordsPROTEIN BINDING / BRD9 / bromodomain / inhibitor
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / 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
Ministry of Science and Technology (MoST, China)2022YFE0210600 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
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 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 9
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7706
Polymers34,8672
Non-polymers9034
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.820, 68.290, 145.650
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
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-A1EFZ / 1-[1-[4-(imidazol-1-ylmethyl)-3,5-dimethoxy-phenyl]indolizin-3-yl]propan-1-one


Mass: 389.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 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: 2.68→72.82 Å / Num. obs: 8990 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.03 / Rrim(I) all: 0.087 / Net I/σ(I): 15.6 / Num. measured all: 74423
Reflection shellResolution: 2.68→2.81 Å / % possible obs: 99.8 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.638 / Num. measured all: 9564 / Num. unique obs: 1147 / CC1/2: 0.828 / Rpim(I) all: 0.236 / Rrim(I) all: 0.682 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→72.82 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.886 / SU B: 14.626 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.775 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29959 460 5.1 %RANDOM
Rwork0.24978 ---
obs0.25249 8490 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å2-0 Å2
2---2.73 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.68→72.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 66 5 1779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191822
X-RAY DIFFRACTIONr_bond_other_d0.0030.021719
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.0072445
X-RAY DIFFRACTIONr_angle_other_deg0.9933.0083991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78323.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29115332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.087158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211947
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02383
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_it4.1417.102834
X-RAY DIFFRACTIONr_mcbond_other4.1077.1833
X-RAY DIFFRACTIONr_mcangle_it6.40910.6471039
X-RAY DIFFRACTIONr_mcangle_other6.41610.6511040
X-RAY DIFFRACTIONr_scbond_it3.8417.252988
X-RAY DIFFRACTIONr_scbond_other3.8417.252988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.09710.7251407
X-RAY DIFFRACTIONr_long_range_B_refined8.64180.6622087
X-RAY DIFFRACTIONr_long_range_B_other8.6480.6672088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6320 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.68→2.747 Å
RfactorNum. reflection% reflection
Rfree0.35 30 -
Rwork0.306 623 -
obs--99.39 %

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