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- PDB-5i40: BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]... -

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Basic information

Entry
Database: PDB / ID: 5i40
TitleBRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one)
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-67N / DI(HYDROXYETHYL)ETHER / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.0402 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 11, 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)12,3597
Polymers11,8571
Non-polymers5036
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint14 kcal/mol
Surface area6100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.580, 33.745, 39.503
Angle α, β, γ (deg.)70.470, 73.320, 74.520
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: 11856.921 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-67N / 6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one


Mass: 148.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 49.79 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M sodium formate 10-15% PEG3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 49565 / % possible obs: 91.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.029 / Rrim(I) all: 0.051 / Χ2: 1.334 / Net I/av σ(I): 29.167 / Net I/σ(I): 10.5 / Num. measured all: 145238
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.04-1.082.70.452185.4
1.08-1.122.90.268188.8
1.12-1.1730.184189.9
1.17-1.2330.149191.1
1.23-1.3130.12191.7
1.31-1.412.90.095192.5
1.41-1.552.90.067193.8
1.55-1.782.90.054194.1
1.78-2.242.90.036194.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.0402→23.12 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 14.91
RfactorNum. reflection% reflection
Rfree0.1595 2458 4.96 %
Rwork0.1319 --
obs0.1333 49561 91.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.26 Å2 / Biso mean: 15.6803 Å2 / Biso min: 7.4 Å2
Refinement stepCycle: final / Resolution: 1.0402→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 37 199 1053
Biso mean--19.61 28.2 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004921
X-RAY DIFFRACTIONf_angle_d0.6991240
X-RAY DIFFRACTIONf_chiral_restr0.062132
X-RAY DIFFRACTIONf_plane_restr0.005158
X-RAY DIFFRACTIONf_dihedral_angle_d17.005356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0402-1.06030.31721150.29232355247082
1.0603-1.08190.26531210.22712487260887
1.0819-1.10540.19771240.18372547267189
1.1054-1.13110.17981140.15622622273690
1.1311-1.15940.17881460.14782513265989
1.1594-1.19080.16751380.1422576271491
1.1908-1.22580.16191360.13272607274391
1.2258-1.26540.13261340.12222604273891
1.2654-1.31060.171650.12072574273992
1.3106-1.36310.13711400.11722691283193
1.3631-1.42510.14391510.11682603275493
1.4251-1.50020.12511160.1142694281094
1.5002-1.59420.12651650.10982644280994
1.5942-1.71720.13971410.11872708284994
1.7172-1.890.13881460.12332695284195
1.89-2.16330.15461250.12052683280894
2.1633-2.72480.1721520.13582793294598
2.7248-23.12570.16991290.13572707283695

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