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- PDB-7nq7: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-N-ethyl-3-(1-methyl... -

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Basic information

Entry
Database: PDB / ID: 7nq7
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-N-ethyl-3-(1-methyl-1H-1,2,3-triazol-4-yl)-4-(1-phenylethoxy)benzamide
ComponentsBromodomain-containing protein 2BRD2
KeywordsNUCLEAR PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD2 / BROMODOMAIN CONTAINING PROTEIN 2 / 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-UL8 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Template-Hopping Approach Leads to Potent, Selective, and Highly Soluble Bromo and Extraterminal Domain (BET) Second Bromodomain (BD2) Inhibitors.
Authors: Aylott, H.E. / Atkinson, S.J. / Bamborough, P. / Bassil, A. / Chung, C.W. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Messenger, C. / Mitchell, D. / Phillipou, ...Authors: Aylott, H.E. / Atkinson, S.J. / Bamborough, P. / Bassil, A. / Chung, C.W. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Messenger, C. / Mitchell, D. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rianjongdee, F. / Rioja, I. / Seal, J.T. / Wall, I.D. / Watson, R.J. / Woolven, J.M. / Demont, E.H.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9695
Polymers13,4321
Non-polymers5374
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint5 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.615, 52.296, 31.882
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
11AAA-782-

HOH

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Components

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


Mass: 13432.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UL8 / ~{N}-ethyl-3-(1-methyl-1,2,3-triazol-4-yl)-4-[(1~{S})-1-phenylethoxy]benzamide


Mass: 350.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% PEG 300, 0.1M MES buffer pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→28.55 Å / Num. obs: 12655 / % possible obs: 92.5 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2459 / CC1/2: 0.587 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→28.55 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.797 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2321 633 5.05 %
Rwork0.1706 11902 -
all0.174 --
obs-12535 90.768 %
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: 25.325 Å2
Baniso -1Baniso -2Baniso -3
1-0.227 Å20 Å2-0 Å2
2---0.193 Å20 Å2
3----0.033 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 38 218 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131046
X-RAY DIFFRACTIONr_bond_other_d0.0010.017968
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.6461407
X-RAY DIFFRACTIONr_angle_other_deg1.2921.6242246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.885122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64321.18659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.673158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_nbd_refined0.1990.2235
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.2842
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2496
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.221
X-RAY DIFFRACTIONr_nbd_other0.1770.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_mcbond_it1.4172.722476
X-RAY DIFFRACTIONr_mcbond_other1.3992.712475
X-RAY DIFFRACTIONr_mcangle_it2.3526.102602
X-RAY DIFFRACTIONr_mcangle_other2.3556.117603
X-RAY DIFFRACTIONr_scbond_it1.7043.111570
X-RAY DIFFRACTIONr_scbond_other1.7033.111570
X-RAY DIFFRACTIONr_scangle_it2.8096.736805
X-RAY DIFFRACTIONr_scangle_other2.8086.735806
X-RAY DIFFRACTIONr_lrange_it5.86626.7261302
X-RAY DIFFRACTIONr_lrange_other5.86426.7291303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7420.25420.25818X-RAY DIFFRACTION84.7291
1.742-1.790.299400.227814X-RAY DIFFRACTION88.3144
1.79-1.8420.253510.206790X-RAY DIFFRACTION89.6589
1.842-1.8980.234450.201776X-RAY DIFFRACTION89.7268
1.898-1.9610.233420.177766X-RAY DIFFRACTION89.6781
1.961-2.0290.213320.18747X-RAY DIFFRACTION90.5814
2.029-2.1060.272400.173730X-RAY DIFFRACTION90.6949
2.106-2.1920.212360.163715X-RAY DIFFRACTION91.6972
2.192-2.2890.15430.15662X-RAY DIFFRACTION91.3212
2.289-2.4010.23330.16646X-RAY DIFFRACTION92.1303
2.401-2.530.276290.163633X-RAY DIFFRACTION92.7171
2.53-2.6840.228270.152605X-RAY DIFFRACTION92.3977
2.684-2.8690.209300.166562X-RAY DIFFRACTION93.2283
2.869-3.0980.234370.174513X-RAY DIFFRACTION92.9054
3.098-3.3930.14250.14490X-RAY DIFFRACTION93.1284
3.393-3.7930.299240.154451X-RAY DIFFRACTION94.8104
3.793-4.3770.242130.155414X-RAY DIFFRACTION92.0259
4.377-5.3560.219190.164343X-RAY DIFFRACTION94.2708
5.356-7.5540.287180.207279X-RAY DIFFRACTION95.1923
7.554-28.550.34870.178148X-RAY DIFFRACTION79.0816
Refinement TLS params.Method: refined / Origin x: 32.5676 Å / Origin y: 9.9088 Å / Origin z: 0.4983 Å
111213212223313233
T0.0096 Å2-0.0073 Å20.0079 Å2-0.0279 Å2-0.0012 Å2--0.0082 Å2
L0.8949 °2-0.0801 °20.1398 °2-0.3196 °20.0914 °2--0.0569 °2
S0.0252 Å °0.0126 Å °0.01 Å °-0.0036 Å °-0.0203 Å °-0.0052 Å °0.002 Å °-0.0012 Å °-0.0049 Å °
Refinement TLS groupSelection: ALL

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