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- PDB-7oep: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-(1,3-dimethoxyprop... -

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Basic information

Entry
Database: PDB / ID: 7oep
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one
ComponentsBromodomain-containing protein 2
KeywordsNUCLEAR PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD2 / BROMODOMAIN CONTAINING PROTEIN 2 / ANTAGONIST
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / : / histone reader activity / neural tube closure / nucleosome assembly / spermatogenesis ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / : / histone reader activity / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain (BrD) profile. / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-NV2 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.801 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)14,4006
Polymers13,4321
Non-polymers9675
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint7 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.735, 53.152, 32.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 2 / 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


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


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-NV2 / 5-[1-(1,3-dimethoxypropan-2-yl)-5-morpholin-4-yl-benzimidazol-2-yl]-1,3-dimethyl-pyridin-2-one / 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one


Mass: 426.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
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 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→26.58 Å / Num. obs: 11665 / % possible obs: 98.5 % / Redundancy: 2.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5 / Num. unique obs: 2773 / CC1/2: 0.765 / % possible all: 99.4

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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: 1.801→26.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.879 / SU B: 4.627 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.148
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.237 570 4.969 %
Rwork0.1734 10901 -
all0.176 --
obs-11471 96.419 %
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: 17.987 Å2
Baniso -1Baniso -2Baniso -3
1-0.326 Å20 Å2-0 Å2
2---0.312 Å20 Å2
3----0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.801→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 67 222 1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131041
X-RAY DIFFRACTIONr_bond_other_d0.0020.017977
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.6561390
X-RAY DIFFRACTIONr_angle_other_deg1.2551.6312272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1465116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36321.60756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.699157
X-RAY DIFFRACTIONr_chiral_restr0.0710.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
X-RAY DIFFRACTIONr_nbd_refined0.1970.2227
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.2878
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2495
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2131
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.29
X-RAY DIFFRACTIONr_nbd_other0.1920.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.227
X-RAY DIFFRACTIONr_mcbond_it0.961.703461
X-RAY DIFFRACTIONr_mcbond_other0.9561.695460
X-RAY DIFFRACTIONr_mcangle_it1.6753.805578
X-RAY DIFFRACTIONr_mcangle_other1.6763.819579
X-RAY DIFFRACTIONr_scbond_it1.3172.07580
X-RAY DIFFRACTIONr_scbond_other1.3162.07581
X-RAY DIFFRACTIONr_scangle_it2.1994.394812
X-RAY DIFFRACTIONr_scangle_other2.1974.394813
X-RAY DIFFRACTIONr_lrange_it5.84817.9111297
X-RAY DIFFRACTIONr_lrange_other5.84617.9141298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.8470.231420.128806X-RAY DIFFRACTION98.6047
1.847-1.8980.248490.198782X-RAY DIFFRACTION97.4209
1.898-1.9530.233270.2747X-RAY DIFFRACTION97.604
1.953-2.0130.407510.221744X-RAY DIFFRACTION98.513
2.013-2.0780.221370.215704X-RAY DIFFRACTION96.9895
2.078-2.1510.271390.19688X-RAY DIFFRACTION98.5095
2.151-2.2320.206400.174659X-RAY DIFFRACTION97.7622
2.232-2.3230.23360.166650X-RAY DIFFRACTION98
2.323-2.4260.176220.168626X-RAY DIFFRACTION97.5904
2.426-2.5440.323290.161603X-RAY DIFFRACTION96.9325
2.544-2.6810.255360.168567X-RAY DIFFRACTION97.5728
2.681-2.8430.293320.167524X-RAY DIFFRACTION97.0332
2.843-3.0380.192240.169507X-RAY DIFFRACTION97.7901
3.038-3.2810.207210.154489X-RAY DIFFRACTION96.5909
3.281-3.5920.199250.153429X-RAY DIFFRACTION94.9791
3.592-4.0120.175210.149382X-RAY DIFFRACTION91.3832
4.012-4.6260.198150.155344X-RAY DIFFRACTION91.5816
4.626-5.6490.24110.184293X-RAY DIFFRACTION91.018
5.649-7.920.293100.201225X-RAY DIFFRACTION86.3971
7.92-260.130.1132X-RAY DIFFRACTION78.9474
Refinement TLS params.Method: refined / Origin x: 32.7222 Å / Origin y: 10.0162 Å / Origin z: 0.5002 Å
111213212223313233
T0.0101 Å2-0.0047 Å2-0.0036 Å2-0.0411 Å2-0.0033 Å2--0.0058 Å2
L0.5649 °20.0465 °20.0989 °2-0.4558 °2-0.0165 °2--0.0302 °2
S0.0202 Å °0.0059 Å °-0.0138 Å °-0.0166 Å °-0.0097 Å °0.0067 Å °0.0106 Å °-0.0007 Å °-0.0105 Å °
Refinement TLS groupSelection: ALL

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