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- PDB-4uiw: BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-ethyl... -

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Basic information

Entry
Database: PDB / ID: 4uiw
TitleBROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-ethyl-4- oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c-pyridine-2- carboximidamide
ComponentsBROMODOMAIN-CONTAINING PROTEIN 9
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / : / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-H1B / Bromodomain-containing protein 9 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsChung, C. / Theodoulou, N.T. / Bamborough, P. / Humphreys, P.G.
CitationJournal: J.Med.Chem. / Year: 2016
Title: The Discovery of I-Brd9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition.
Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / ...Authors: Theodoulou, N.H. / Bamborough, P. / Bannister, A.J. / Becher, I. / Bit, R.A. / Che, K.H. / Chung, C. / Dittmann, A. / Drewes, G. / Drewry, D.H. / Gordon, L. / Grandi, P. / Leveridge, M. / Lindon, M. / Michon, A. / Molnar, J. / Robson, S.C. / Tomkinson, N.C.O. / Kouzarides, T. / Prinjha, R.K. / Humphreys, P.G.
History
DepositionApr 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)12,7883
Polymers12,2281
Non-polymers5602
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.689, 33.918, 39.578
Angle α, β, γ (deg.)68.84, 73.76, 73.83
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 / HUMAN BRD9


Mass: 12228.203 Da / Num. of mol.: 1 / Fragment: RESIDUES 133-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A6NFY8, UniProt: Q9H8M2*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-H1B / N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide


Mass: 497.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22F3N3O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.38 Å3/Da / Density % sol: 48.29 % / Description: NONE
Crystal growTemperature: 277 K / pH: 6.5
Details: 0.1M MORPHEUS BUFFER PH 6.5, 30% MORPHEUS_EDO_P8K, 0.1M MORPHEUS AMINO ACIDS AT 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54178
DetectorDate: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→31 Å / Num. obs: 10779 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 26.1
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 7.6 / % possible all: 85.3

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.73→31 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.561 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17951 505 4.7 %RANDOM
Rwork0.1347 ---
obs0.13681 10155 91.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.298 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0.09 Å2-0.04 Å2
2---0.03 Å2-0.16 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.73→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 0 37 224 1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019915
X-RAY DIFFRACTIONr_bond_other_d0.0010.02645
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9511245
X-RAY DIFFRACTIONr_angle_other_deg12.9951579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9455112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82623.78437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28415166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.117153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0560.021982
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: 1.733→1.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 32 -
Rwork0.201 687 -
obs--82.93 %
Refinement TLS params.Method: refined / Origin x: -5.2169 Å / Origin y: 5.536 Å / Origin z: 3.2519 Å
111213212223313233
T0.0246 Å20.0006 Å2-0.0052 Å2-0.008 Å20.0036 Å2--0.0073 Å2
L0.9236 °20.0963 °2-0.18 °2-0.3229 °20.2022 °2--0.1924 °2
S0.0095 Å °-0.0263 Å °0.044 Å °-0.0156 Å °-0.0078 Å °0.016 Å °-0.0081 Å °0.0015 Å °-0.0017 Å °

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