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- PDB-5mky: BROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2... -

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Basic information

Entry
Database: PDB / ID: 5mky
TitleBROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2,3,4-tetrahydroisoquinolin-5-yl)amino)pyridazin-3(2H)-one
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / BRD9 / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN
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-I0D / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.67 Å
AuthorsChung, C.-W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe.
Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. ...Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. / Tough, D.F. / Prinjha, R.K.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 13, 2022Group: Advisory / Database references / Structure summary
Category: audit_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)12,8383
Polymers12,2281
Non-polymers6102
Water3,891216
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.551, 34.076, 39.750
Angle α, β, γ (deg.)68.21, 76.01, 73.37
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: 12228.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8M2
#2: Chemical ChemComp-I0D / 4-chloranyl-2-methyl-5-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-5-yl)amino]pyridazin-3-one


Mass: 304.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17ClN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus condition 54 - 0.1M morpheus buffer 2 pH 7.5, 30% morpheus_EDO_P8K, 0.1M Morpheus ethylene glycols

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.67→36.48 Å / Num. obs: 11611 / % possible obs: 88.3 % / Redundancy: 2.19 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.6
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 4.1 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.67→36.48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.935 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22047 567 4.9 %RANDOM
Rwork0.16905 ---
obs0.17153 11044 88.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20.07 Å2-0.07 Å2
2--0.68 Å2-0.85 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.67→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 42 216 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019905
X-RAY DIFFRACTIONr_bond_other_d0.0010.02627
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9271226
X-RAY DIFFRACTIONr_angle_other_deg0.83631531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7285106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90423.94738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.134153
X-RAY DIFFRACTIONr_chiral_restr0.0680.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 37 -
Rwork0.231 777 -
obs--83.83 %
Refinement TLS params.Method: refined / Origin x: -5.1069 Å / Origin y: 7.2051 Å / Origin z: 2.9591 Å
111213212223313233
T0.0233 Å20.0002 Å2-0.0065 Å2-0.003 Å2-0.0034 Å2--0.0181 Å2
L0.7413 °20.111 °2-0.0988 °2-0.2884 °20.3488 °2--0.5135 °2
S0.0271 Å °-0.0406 Å °0.0297 Å °-0.0063 Å °-0.0184 Å °0.0065 Å °-0.0001 Å °-0.0103 Å °-0.0087 Å °

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