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- PDB-5f1l: Crystal structure of the bromodomain of BRD9 in complex with comp... -

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Basic information

Entry
Database: PDB / ID: 5f1l
TitleCrystal structure of the bromodomain of BRD9 in complex with compound 9.
ComponentsBromodomain-containing protein 9
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 / chromatin / positive regulation of cell population proliferation / 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 / chromatin / positive regulation of cell population proliferation / 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-5U2 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1884
Polymers28,5002
Non-polymers6892
Water1,22568
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5942
Polymers14,2501
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5942
Polymers14,2501
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.308, 125.165, 30.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 9


Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: Bromodomain, UNP residues 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-5U2 / 5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one


Mass: 344.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
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: Mar 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→125.17 Å / Num. obs: 12714 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 57.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Net I/σ(I): 24.7 / Num. measured all: 79569
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.27-2.546.51.1343.22281434960.9550.47498.3
5.08-125.175.90.02166.7739612640.9990.00999.5

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 2.3→35.88 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9345 / SU R Cruickshank DPI: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.322 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 590 4.83 %RANDOM
Rwork0.1917 ---
obs0.1926 12218 98.27 %-
Displacement parametersBiso max: 155.79 Å2 / Biso mean: 70.23 Å2 / Biso min: 32.77 Å2
Baniso -1Baniso -2Baniso -3
1--7.7313 Å20 Å20 Å2
2--18.6031 Å20 Å2
3----10.8718 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.3→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 50 68 1037
Biso mean--68.98 62.57 -
Num. residues----227
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d699SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes279HARMONIC5
X-RAY DIFFRACTIONt_it1951HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion242SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2251SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1951HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg2621HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2
X-RAY DIFFRACTIONt_other_torsion19.65
LS refinement shellResolution: 2.3→2.52 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.223 120 4.22 %
Rwork0.2343 2723 -
all0.2338 2843 -
obs--98.27 %
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)
12.3942-2.2832-1.249115.19013.03551.7469-0.00180.0080.07430.8050.03550.438-0.0228-0.4482-0.0337-0.11270.15660.0392-0.04170.0406-0.235715.98188.24246.3443
24.0193-3.22780.641510.2263-0.26842.2448-0.1675-0.1725-0.22420.3930.17130.36180.35430.0357-0.0038-0.01860.00940.112-0.1624-0.0176-0.19597.83742.01847.6324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 134
2X-RAY DIFFRACTION2{ B|* }B21 - 134

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