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- PDB-5f25: Crystal structure of the BRD9 bromodomain in complex with compound 4. -

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Basic information

Entry
Database: PDB / ID: 5f25
TitleCrystal structure of the BRD9 bromodomain in complex with compound 4.
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-5TU / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBader, G. / Martin, L.J. / 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
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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)28,9844
Polymers28,5002
Non-polymers4852
Water5,513306
1
A: BRD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4922
Polymers14,2501
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRD9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4922
Polymers14,2501
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.038, 125.017, 29.941
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-390-

HOH

21B-452-

HOH

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Components

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


Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: bromodomain
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-5TU / 4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide


Mass: 242.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: glycerol ethoxylate, 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 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→27.03 Å / Num. obs: 31467 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.013 / Net I/σ(I): 30.9 / Num. measured all: 197150 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.68-1.816.30.5213.63980763490.950.224100
4.44-27.035.60.01494.110441186910.00799.5

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.68→27.03 Å / Cor.coef. Fo:Fc: 0.9511 / Cor.coef. Fo:Fc free: 0.9517 / SU R Cruickshank DPI: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.108 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1575 5.03 %RANDOM
Rwork0.1892 ---
obs0.1901 31342 99.88 %-
Displacement parametersBiso max: 105.82 Å2 / Biso mean: 38.09 Å2 / Biso min: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.9005 Å20 Å20 Å2
2--8.7419 Å20 Å2
3----6.8413 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: final / Resolution: 1.68→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 36 306 2159
Biso mean--34.64 46.45 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d661SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes274HARMONIC5
X-RAY DIFFRACTIONt_it1896HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
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_contact2406SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1896HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2551HARMONIC20.81
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion15.04
LS refinement shellResolution: 1.68→1.74 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.217 123 4.34 %
Rwork0.2273 2708 -
all0.2269 2831 -
obs--99.88 %
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)
11.1987-0.6108-0.39175.7042-0.02140.73540.107-0.03030.14640.33770.04880.4219-0.0984-0.2413-0.1558-0.06120.06960.0515-0.05190.0145-0.05116.50958.35346.1282
22.3307-1.36860.54285.21790.36051.6767-0.1759-0.0577-0.25890.06640.06220.22370.1942-0.04760.1137-0.05980.00660.0626-0.1097-0.0024-0.05547.639642.07447.5846
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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