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- PDB-4uix: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)... -

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Basic information

Entry
Database: PDB / ID: 4uix
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-c-pyridine-2- carboxamide
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-TVU / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 4
B: BROMODOMAIN-CONTAINING PROTEIN 4
C: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,99711
Polymers45,3013
Non-polymers1,6968
Water7,710428
1
A: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6794
Polymers15,1001
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6794
Polymers15,1001
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6393
Polymers15,1001
Non-polymers5392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.640, 44.670, 77.550
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 4 / PROTEIN HUNK1 / NHUMAN BRD4


Mass: 15100.431 Da / Num. of mol.: 3 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TVU / N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide


Mass: 476.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H24N2O6S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.43 Å3/Da / Density % sol: 49.45 % / Description: NONE
Crystal growTemperature: 293 K / Details: 0.2M CACL2, 0.1M HEPES, PEG 6K 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.58→49.23 Å / Num. obs: 58489 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.4
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→49.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.272 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23788 2958 5.1 %RANDOM
Rwork0.19993 ---
obs0.2019 55517 97.34 %-
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: 21.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.25 Å2
2--0.92 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3071 0 110 428 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193299
X-RAY DIFFRACTIONr_bond_other_d0.0010.022267
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9644496
X-RAY DIFFRACTIONr_angle_other_deg0.83635574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0425371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91325.742155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.803159
X-RAY DIFFRACTIONr_chiral_restr0.0630.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
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: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 180 -
Rwork0.228 3973 -
obs--96.85 %
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)
10.17460.01280.1220.46020.34120.6026-0.04110.0077-0.0109-0.023-0.01270.0356-0.06740.0310.05380.0485-0.0041-0.01690.0064-0.0030.042124.93766.090628.2101
20.3147-0.06150.13920.1286-0.32090.8627-0.0177-0.0109-0.0108-0.01410.0283-0.01440.0274-0.0588-0.01050.03270.0010.00550.0206-0.00830.04253.647527.724623.2063
31.41180.3474-1.3531.3195-0.84221.5158-0.0719-0.0926-0.1979-0.0206-0.06740.09710.06040.12290.13930.0229-0.00280.01080.04470.03730.0715-17.451314.29867.1332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 168
2X-RAY DIFFRACTION2B42 - 167
3X-RAY DIFFRACTION3C42 - 163

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