[English] 日本語
Yorodumi
- PDB-7oep: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 5-(1-(1,3-dimethoxyprop... -

+
Open data


ID or keywords:

Loading...

-
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 / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / 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 serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / 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 / Bromodomain profile. / bromo domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more