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- PDB-6yqw: BRD9 with 4-chloro-2-methyl-methylamino-pyridazinone -

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Basic information

Entry
Database: PDB / ID: 6yqw
TitleBRD9 with 4-chloro-2-methyl-methylamino-pyridazinone
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / BRD9 / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-82I / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Application of Atypical Acetyl-lysine Methyl Mimetics in the Development of Selective Inhibitors of the Bromodomain-Containing Protein 7 (BRD7)/Bromodomain-Containing Protein 9 (BRD9) Bromodomains.
Authors: Clegg, M.A. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Liwicki, G.M. / Michon, A.M. / Molnar, J. / Rioja, I. / Soden, P.E. / ...Authors: Clegg, M.A. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Liwicki, G.M. / Michon, A.M. / Molnar, J. / Rioja, I. / Soden, P.E. / Theodoulou, N.H. / Werner, T. / Tomkinson, N.C.O. / Prinjha, R.K. / Humphreys, P.G.
History
DepositionApr 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)12,4022
Polymers12,2281
Non-polymers1741
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.566, 33.928, 39.623
Angle α, β, γ (deg.)70.450, 73.630, 74.390
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 12228.203 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-82I / 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one


Mass: 173.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M morpheus buffer 3, pH 8.5, 30% morpheus_EDO_p8K, 0.1M morpheus alcohol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→27.98 Å / Num. obs: 17167 / % possible obs: 94.3 % / Redundancy: 1.7 % / Biso Wilson estimate: 8.26 Å2 / Rpim(I) all: 0.095 / Rrim(I) all: 0.134 / Rsym value: 0.095 / Net I/av σ(I): 3.8 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.581.70.1723.4421124900.1720.2430.1724.592.8
1.58-1.681.80.0913.9415123430.0910.1290.0914.593.6
1.68-1.791.70.115.7372322050.110.1550.114.993.5
1.79-1.941.70.1273.3352420600.1270.1790.1275.793.7
1.94-2.121.80.1483343319290.1480.2090.148694.6
2.12-2.371.70.1342.7296917390.1340.190.1346.195.9
2.37-2.741.80.0696.4274615620.0690.0980.0696.496.5
2.74-3.351.70.0511.4227113220.050.0710.056.597.2
3.35-4.741.70.0569.5174210110.0560.080.0566.696.1
4.74-27.9751.60.04211.48195060.0420.0590.0426.488.5

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER2.11.1refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house model

Resolution: 1.5→27.98 Å / Cor.coef. Fo:Fc: 0.8573 / Cor.coef. Fo:Fc free: 0.8255 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 874 5.1 %RANDOM
Rwork0.2388 ---
obs0.2407 17133 94.17 %-
Displacement parametersBiso max: 93.81 Å2 / Biso mean: 12 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--0.1271 Å2-0.0696 Å2-1.0247 Å2
2---0.3296 Å20.7635 Å2
3---0.4566 Å2
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: final / Resolution: 1.5→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 11 208 1040
Biso mean--6.25 23.89 -
Num. residues----101
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4116 134 4.95 %
Rwork0.373 2571 -
all0.3748 2705 -
obs--94.17 %

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