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- PDB-5i7x: BRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dih... -

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Basic information

Entry
Database: PDB / ID: 5i7x
TitleBRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide)
ComponentsBromodomain-containing protein 9
KeywordsRNA BINDING PROTEIN / Bromodomain Inhibitor Epigenetics Structure-based drug design
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-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-67B / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1752 Å
AuthorsMurray, J.M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.
Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / ...Authors: Crawford, T.D. / Tsui, V. / Flynn, E.M. / Wang, S. / Taylor, A.M. / Cote, A. / Audia, J.E. / Beresini, M.H. / Burdick, D.J. / Cummings, R. / Dakin, L.A. / Duplessis, M. / Good, A.C. / Hewitt, M.C. / Huang, H.R. / Jayaram, H. / Kiefer, J.R. / Jiang, Y. / Murray, J. / Nasveschuk, C.G. / Pardo, E. / Poy, F. / Romero, F.A. / Tang, Y. / Wang, J. / Xu, Z. / Zawadzke, L.E. / Zhu, X. / Albrecht, B.K. / Magnuson, S.R. / Bellon, S. / Cochran, A.G.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)12,0232
Polymers11,7281
Non-polymers2951
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.640, 34.000, 39.490
Angle α, β, γ (deg.)68.560, 74.310, 72.950
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: 11727.741 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-67B / N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide


Mass: 295.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.175→18.067 Å / Num. obs: 32239 / % possible obs: 86.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.066 / Rrim(I) all: 0.112 / Net I/σ(I): 5.8 / Num. measured all: 83751
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.175-1.1792.50.4018423310.8630.3160.5122.187.1
5.406-18.0672.40.0736682730.980.0520.096.572

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1752→18.067 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 16.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1681 1625 5.04 %
Rwork0.152 30611 -
obs0.1528 32236 86.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.54 Å2 / Biso mean: 16.8735 Å2 / Biso min: 6.78 Å2
Refinement stepCycle: final / Resolution: 1.1752→18.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms813 0 23 187 1023
Biso mean--15.54 28.26 -
Num. residues----101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003877
X-RAY DIFFRACTIONf_angle_d0.6691185
X-RAY DIFFRACTIONf_chiral_restr0.063124
X-RAY DIFFRACTIONf_plane_restr0.006151
X-RAY DIFFRACTIONf_dihedral_angle_d15.094321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1752-1.20980.21491300.20842556268687
1.2098-1.24880.21441410.19542591273287
1.2488-1.29350.17921470.18422573272087
1.2935-1.34520.21061570.17162543270087
1.3452-1.40640.16541240.1542602272688
1.4064-1.48050.17681320.14252604273687
1.4805-1.57330.18361330.13382560269387
1.5733-1.69460.15511320.12852607273987
1.6946-1.8650.15791370.13742562269987
1.865-2.13450.14821400.13282467260784
2.1345-2.68790.16561400.15312389252981
2.6879-18.06890.16261120.15872557266986

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