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- PDB-7oes: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(meth... -

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Basic information

Entry
Database: PDB / ID: 7oes
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)-6-oxo-N-(2-phenylpropyl)-1,6-dihydropyridine-3-carboxamide
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-VBE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.602 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of a Highly Selective BET BD2 Inhibitor from a DNA-Encoded Library Technology Screening Hit.
Authors: Rianjongdee, F. / Atkinson, S.J. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Kaushansky, L.J. / Medeiros, P. / Messenger, C. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rioja, I. / Satz, ...Authors: Rianjongdee, F. / Atkinson, S.J. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Kaushansky, L.J. / Medeiros, P. / Messenger, C. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rioja, I. / Satz, A.L. / Taylor, S. / Wall, I.D. / Watson, R.J. / Yao, G. / Demont, E.H.
History
DepositionMay 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)14,3296
Polymers13,4321
Non-polymers8965
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint7 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.647, 52.388, 31.987
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-763-

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-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-VBE / 1,5-dimethyl-N-[2-(methylamino)-2-oxidanylidene-ethyl]-6-oxidanylidene-N-[(2S)-2-phenylpropyl]pyridine-3-carboxamide / 1,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)-6-oxo-N-(2-phenylpropyl)-1,6-dihydropyridine-3-carboxamide


Mass: 355.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
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: Oct 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→42.29 Å / Num. obs: 15516 / % possible obs: 94.6 % / Redundancy: 2.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.017 / Net I/σ(I): 33.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 1660 / CC1/2: 0.924 / % possible all: 71

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: in house structure

Resolution: 1.602→32.007 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.422 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1832 741 4.811 %
Rwork0.1549 14661 -
all0.156 --
obs-15402 93.589 %
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: 20.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.078 Å2-0 Å2-0 Å2
2---0.291 Å20 Å2
3---0.369 Å2
Refinement stepCycle: LAST / Resolution: 1.602→32.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 62 185 1170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131045
X-RAY DIFFRACTIONr_bond_other_d0.0010.017980
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.6561397
X-RAY DIFFRACTIONr_angle_other_deg1.2241.6252280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7555119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62321.75457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4115180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.243157
X-RAY DIFFRACTIONr_chiral_restr0.0610.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_nbd_refined0.1940.2226
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.2827
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2492
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2145
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.140.210
X-RAY DIFFRACTIONr_nbd_other0.1460.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0880.229
X-RAY DIFFRACTIONr_mcbond_it1.0932.271467
X-RAY DIFFRACTIONr_mcbond_other1.0732.262466
X-RAY DIFFRACTIONr_mcangle_it1.8735.082589
X-RAY DIFFRACTIONr_mcangle_other1.8775.095590
X-RAY DIFFRACTIONr_scbond_it1.7522.72578
X-RAY DIFFRACTIONr_scbond_other1.7512.719579
X-RAY DIFFRACTIONr_scangle_it2.8555.779808
X-RAY DIFFRACTIONr_scangle_other2.8545.777809
X-RAY DIFFRACTIONr_lrange_it5.7323.0591295
X-RAY DIFFRACTIONr_lrange_other5.72823.0571296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.602-1.6440.246370.195691X-RAY DIFFRACTION61.8522
1.644-1.6890.234460.19882X-RAY DIFFRACTION78.5775
1.689-1.7370.185440.1761010X-RAY DIFFRACTION94.5291
1.737-1.7910.225650.171015X-RAY DIFFRACTION97.035
1.791-1.8490.196420.1561001X-RAY DIFFRACTION98.7689
1.849-1.9140.153410.16982X-RAY DIFFRACTION98.4601
1.914-1.9860.177380.154937X-RAY DIFFRACTION98.3855
1.986-2.0670.183430.148916X-RAY DIFFRACTION98.5611
2.067-2.1590.149350.146867X-RAY DIFFRACTION98.4716
2.159-2.2640.171440.139837X-RAY DIFFRACTION98.6562
2.264-2.3860.197310.14805X-RAY DIFFRACTION98.9349
2.386-2.530.204460.145760X-RAY DIFFRACTION98.8957
2.53-2.7040.156450.143699X-RAY DIFFRACTION98.6737
2.704-2.920.168350.151679X-RAY DIFFRACTION98.6188
2.92-3.1970.248310.159613X-RAY DIFFRACTION98.4709
3.197-3.5720.169360.148557X-RAY DIFFRACTION98.6689
3.572-4.120.152320.15492X-RAY DIFFRACTION97.5791
4.12-5.0340.231190.148420X-RAY DIFFRACTION95.0216
5.034-7.0690.155230.189314X-RAY DIFFRACTION90.3485
7.069-320.15180.201184X-RAY DIFFRACTION81.0127

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