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

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Basic information

Entry
Database: PDB / ID: 9kly
TitleCrystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22032
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: 2.15 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7732
Polymers17,4331
Non-polymers3391
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.959, 51.056, 64.369
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 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 17433.268 Da / Num. of mol.: 1
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-A1EHA / 1-[1-[2,5-dimethoxy-4-[(1~{S})-1-oxidanylethyl]phenyl]indolizin-3-yl]ethanone


Mass: 339.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 7.0, 20% 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: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→51.06 Å / Num. obs: 7195 / % possible obs: 88.3 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rrim(I) all: 0.049 / Net I/σ(I): 19.8 / Num. measured all: 27123
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 91.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.095 / Num. measured all: 2214 / Num. unique obs: 647 / CC1/2: 0.99 / Rpim(I) all: 0.055 / Rrim(I) all: 0.111 / Net I/σ(I) obs: 10.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.568 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22743 364 5.1 %RANDOM
Rwork0.19006 ---
obs0.19187 6816 86.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.246 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0 Å20 Å2
2--3.15 Å2-0 Å2
3----1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 25 21 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019977
X-RAY DIFFRACTIONr_bond_other_d0.0020.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.4742.0031312
X-RAY DIFFRACTIONr_angle_other_deg0.923.0062166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45923.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.948155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
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_it2.0753.262455
X-RAY DIFFRACTIONr_mcbond_other2.0693.252454
X-RAY DIFFRACTIONr_mcangle_it3.2374.863567
X-RAY DIFFRACTIONr_mcangle_other3.2354.876568
X-RAY DIFFRACTIONr_scbond_it2.7993.67522
X-RAY DIFFRACTIONr_scbond_other2.7963.668523
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6235.306746
X-RAY DIFFRACTIONr_long_range_B_refined5.98836.3961101
X-RAY DIFFRACTIONr_long_range_B_other5.99636.3491097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 34 -
Rwork0.212 509 -
obs--89.75 %

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