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- PDB-6tq2: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(4-(4-fluorophenyl)-1... -

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Basic information

Entry
Database: PDB / ID: 6tq2
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(4-(4-fluorophenyl)-1H-imidazol-5-yl)-1-methylpyridin-2(1H)-one
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-NUQ / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.26 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment Screening.
Authors: Wellaway, C.R. / Amans, D. / Bamborough, P. / Barnett, H. / Bit, R.A. / Brown, J.A. / Carlson, N.R. / Chung, C.W. / Cooper, A.W.J. / Craggs, P.D. / Davis, R.P. / Dean, T.W. / Evans, J.P. / ...Authors: Wellaway, C.R. / Amans, D. / Bamborough, P. / Barnett, H. / Bit, R.A. / Brown, J.A. / Carlson, N.R. / Chung, C.W. / Cooper, A.W.J. / Craggs, P.D. / Davis, R.P. / Dean, T.W. / Evans, J.P. / Gordon, L. / Harada, I.L. / Hirst, D.J. / Humphreys, P.G. / Jones, K.L. / Lewis, A.J. / Lindon, M.J. / Lugo, D. / Mahmood, M. / McCleary, S. / Medeiros, P. / Mitchell, D.J. / O'Sullivan, M. / Le Gall, A. / Patel, V.K. / Patten, C. / Poole, D.L. / Shah, R.R. / Smith, J.E. / Stafford, K.A.J. / Thomas, P.J. / Vimal, M. / Wall, I.D. / Watson, R.J. / Wellaway, N. / Yao, G. / Prinjha, R.K.
History
DepositionDec 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 2
BBB: Bromodomain-containing protein 2
CCC: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,37411
Polymers54,1203
Non-polymers1,2548
Water5,981332
1
AAA: Bromodomain-containing protein 2
BBB: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8737
Polymers36,0802
Non-polymers7935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-33 kcal/mol
Surface area11960 Å2
MethodPISA
2
CCC: Bromodomain-containing protein 2
hetero molecules

CCC: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0038
Polymers36,0802
Non-polymers9236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2860 Å2
ΔGint-58 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.790, 55.850, 67.440
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11CCC-434-

HOH

21CCC-462-

HOH

31CCC-468-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 18039.926 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3
Production host: Escherichia coli str. 'clone D i14' (bacteria)
References: UniProt: P25440
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NUQ / 5-[5-(4-fluorophenyl)-1~{H}-imidazol-4-yl]-1-methyl-pyridin-2-one


Mass: 269.274 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H12FN3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Hepes pH 7.0, 24-28% PEG3350, 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→50.28 Å / Num. obs: 20095 / % possible obs: 98.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2923 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: not published

Resolution: 2.26→40.893 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.286 / WRfactor Rwork: 0.216 / SU B: 7.735 / SU ML: 0.193 / Average fsc free: 0.8748 / Average fsc work: 0.9061 / Cross valid method: FREE R-VALUE / ESU R: 0.34 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2691 1022 5.087 %
Rwork0.2018 19070 -
all0.205 --
obs-20092 98.776 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 54.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.174 Å20 Å2-0.124 Å2
2---0.213 Å2-0 Å2
3---0.056 Å2
Refinement stepCycle: LAST / Resolution: 2.26→40.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 84 332 3193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172708
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.6524061
X-RAY DIFFRACTIONr_angle_other_deg1.1741.5936312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86124.052153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44415539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6461510
X-RAY DIFFRACTIONr_chiral_restr0.050.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023258
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02619
X-RAY DIFFRACTIONr_nbd_refined0.1820.2655
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.22427
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21397
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.222
X-RAY DIFFRACTIONr_nbd_other0.2150.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.220
X-RAY DIFFRACTIONr_mcbond_it4.1557.3171355
X-RAY DIFFRACTIONr_mcbond_other4.1487.3131354
X-RAY DIFFRACTIONr_mcangle_it6.05316.4131699
X-RAY DIFFRACTIONr_mcangle_other6.05216.4211700
X-RAY DIFFRACTIONr_scbond_it4.4527.9521638
X-RAY DIFFRACTIONr_scbond_other4.457.9551639
X-RAY DIFFRACTIONr_scangle_it6.75617.5522362
X-RAY DIFFRACTIONr_scangle_other6.75517.5572363
X-RAY DIFFRACTIONr_lrange_it9.22665.613635
X-RAY DIFFRACTIONr_lrange_other9.22565.633636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.26-2.3190.349780.22613990.23214970.8560.89598.6640.202
2.319-2.3820.315660.19213700.19814380.850.90499.86090.183
2.382-2.4510.285790.18913170.19514030.8740.90599.50110.18
2.451-2.5260.252720.17212900.17613710.8840.92499.34350.168
2.526-2.6080.277480.19912880.20213400.8340.86999.70150.201
2.608-2.70.436750.28612090.29412880.7450.83199.68940.271
2.7-2.8010.238620.20411680.20612380.8950.88999.35380.212
2.801-2.9150.253690.16611480.17112260.9130.93499.26590.18
2.915-3.0440.306600.16510550.17211190.8890.93699.64250.181
3.044-3.1910.231570.17710410.1811080.9080.93299.09750.195
3.191-3.3630.263530.219980.21310550.8840.90699.62090.234
3.363-3.5650.323600.2439280.2489960.8630.89799.19680.254
3.565-3.8090.219420.2248700.2249280.9120.91698.27590.239
3.809-4.1120.271260.2218290.2238630.8870.93699.0730.238
4.112-4.50.202420.1527630.1548170.940.96198.53120.181
4.5-5.0230.206320.1697010.177420.9510.95498.78710.202
5.023-5.7860.239330.1835700.1866430.920.94293.77920.229
5.786-7.0510.227310.1955220.1975530.9070.9241000.242
7.051-9.8260.299250.2094090.2144420.8510.86498.190.246
9.826-40.8930.277120.2991950.2982690.780.65376.95170.555

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