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- PDB-5eu1: CRYSTAL STRUCTURE OF BRD9 IN COMPLEX WITH BI-7273 -

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Basic information

Entry
Database: PDB / ID: 5eu1
TitleCRYSTAL STRUCTURE OF BRD9 IN COMPLEX WITH BI-7273
ComponentsBRD9
KeywordsTRANSCRIPTION / 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 / 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-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5SW / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBader, G. / Martin, L.M. / Steurer, S. / Weiss-Puxbaum, A. / Zoephel, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor.
Authors: Martin, L.J. / Koegl, M. / Bader, G. / Cockcroft, X.L. / Fedorov, O. / Fiegen, D. / Gerstberger, T. / Hofmann, M.H. / Hohmann, A.F. / Kessler, D. / Knapp, S. / Knesl, P. / Kornigg, S. / ...Authors: Martin, L.J. / Koegl, M. / Bader, G. / Cockcroft, X.L. / Fedorov, O. / Fiegen, D. / Gerstberger, T. / Hofmann, M.H. / Hohmann, A.F. / Kessler, D. / Knapp, S. / Knesl, P. / Kornigg, S. / Muller, S. / Nar, H. / Rogers, C. / Rumpel, K. / Schaaf, O. / Steurer, S. / Tallant, C. / Vakoc, C.R. / Zeeb, M. / Zoephel, A. / Pearson, M. / Boehmelt, G. / McConnell, D.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: BRD9
B: BRD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2064
Polymers28,5002
Non-polymers7072
Water6,341352
1
A: BRD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6032
Polymers14,2501
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6032
Polymers14,2501
Non-polymers3531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.800, 125.359, 29.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

21B-443-

HOH

31B-452-

HOH

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Components

#1: Protein BRD9 / BRD9 / DKFZp434D0711 / DKFZp686L0539 / LAVS3040 / PRO9856


Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: UNP residues 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-5SW / 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one


Mass: 353.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 30 % glycerol ethoxylate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→36 Å / Num. obs: 35816 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 26.2
Reflection shellResolution: 1.6→1.79 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.9582 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 1784 4.98 %RANDOM
Rwork0.1783 ---
obs0.179 35816 99.04 %-
Displacement parametersBiso max: 116.27 Å2 / Biso mean: 37.65 Å2 / Biso min: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.4387 Å20 Å20 Å2
2--8.0487 Å20 Å2
3----4.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: final / Resolution: 1.6→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 52 352 1323
Biso mean--32.13 47.24 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d700SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1962HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion243SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2524SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1962HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2638HARMONIC20.81
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion15.26
LS refinement shellResolution: 1.6→1.65 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.1795 106 4.05 %
Rwork0.202 2514 -
all0.201 2620 -
obs--99.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4738-0.6965-0.59025.14230.49740.85720.10160.01460.08850.0428-0.01870.2024-0.1399-0.2437-0.0829-0.04880.05620.0005-0.04340.0172-0.078816.28448.54376.1723
22.8949-2.01780.75314.7503-0.49691.4356-0.1914-0.1427-0.130.16560.14750.03650.168-0.03190.0439-0.02080.02070.0487-0.1136-0.0088-0.0918.030842.2487.6395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 134
2X-RAY DIFFRACTION2{ B|* }B21 - 133

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