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- PDB-5f1h: Crystal structure of the BRD9 bromodamian in complex with BI-9564. -

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Basic information

Entry
Database: PDB / ID: 5f1h
TitleCrystal structure of the BRD9 bromodamian in complex with BI-9564.
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 / 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 ...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-5U6 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)29,2064
Polymers28,5002
Non-polymers7072
Water3,747208
1
A: Bromodomain-containing protein 9
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: Bromodomain-containing protein 9
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)70.030, 125.358, 29.681
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-373-

HOH

21B-386-

HOH

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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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-5U6 / 4-[4-[(dimethylamino)methyl]-2,5-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.: 208 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
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: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→70.03 Å / Num. obs: 24239 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Net I/σ(I): 19.9 / Num. measured all: 155044
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
1.82-2.16.40.5233.45362383400.9610.22299.7
3.64-70.0360.02557.41936932360.9990.01199.5

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
BUSTERrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HME

3hme


Resolution: 1.82→35.88 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 1238 5.12 %RANDOM
Rwork0.191 ---
obs0.1916 24186 99.33 %-
Displacement parametersBiso max: 136.28 Å2 / Biso mean: 49.83 Å2 / Biso min: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å20 Å20 Å2
2--12.0071 Å20 Å2
3----7.6572 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: final / Resolution: 1.82→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 52 208 1179
Biso mean--43.47 53.11 -
Num. residues----226
LS refinement shellResolution: 1.82→1.9 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2563 159 5.58 %
Rwork0.2237 2691 -
all0.2257 2850 -
obs--99.33 %
Refinement TLS params.

S23: 0.2075 Å ° / 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 °)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)
11.5741-1.0815-0.74538.86691.85811.63560.23730.05240.2159-0.2224-0.1617-0.3185-0.4279-0.0756-0.11050.10210.0252-0.06630.015-0.103715.81538.28596.2521
23.2482-2.02060.36465.6649-0.21592.1063-0.2414-0.0751-0.42160.16150.14720.3666-0.03990.0942-0.00690.00050.0916-0.175-0.0089-0.10317.74442.18097.4948
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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