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

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Basic information

Entry
Database: PDB / ID: 9kla
TitleCrystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22024
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
: / D-MALATE / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2505
Polymers17,4331
Non-polymers8174
Water2,126118
1
A: Bromodomain-containing protein 9
hetero molecules

A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,50010
Polymers34,8672
Non-polymers1,6348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3070 Å2
ΔGint-28 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.220, 58.220, 87.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-A1EF0 / 1-[1-(3,5-dimethoxyphenyl)indolizin-3-yl]ethanone


Mass: 295.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M DL-Malic acid 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: 0.97919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.78→50.42 Å / Num. obs: 16479 / % possible obs: 97.4 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.036 / Rrim(I) all: 0.104 / Χ2: 1.01 / Net I/σ(I): 12.5 / Num. measured all: 135948
Reflection shellResolution: 1.78→1.82 Å / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.954 / Num. measured all: 6157 / Num. unique obs: 918 / CC1/2: 0.669 / Rpim(I) all: 0.377 / Rrim(I) all: 1.03 / Χ2: 0.83 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→43.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.457 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23154 800 4.9 %RANDOM
Rwork0.19366 ---
obs0.19542 15660 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.078 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å2-0 Å2
2--0.48 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.78→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 65 119 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131160
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181091
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.7141551
X-RAY DIFFRACTIONr_angle_other_deg1.1941.6342528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.595129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66622.40754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07915212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.282155
X-RAY DIFFRACTIONr_chiral_restr0.0570.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
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_it1.2822.855525
X-RAY DIFFRACTIONr_mcbond_other1.2832.848524
X-RAY DIFFRACTIONr_mcangle_it2.0624.24651
X-RAY DIFFRACTIONr_mcangle_other2.0614.249652
X-RAY DIFFRACTIONr_scbond_it1.8823.154635
X-RAY DIFFRACTIONr_scbond_other1.8813.154636
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1314.607900
X-RAY DIFFRACTIONr_long_range_B_refined4.5832.3311350
X-RAY DIFFRACTIONr_long_range_B_other4.47631.9171325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 53 -
Rwork0.271 1128 -
obs--95.63 %

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