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- PDB-7nqi: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 2-benzyl-N-cyclopropyl-... -

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Basic information

Entry
Database: PDB / ID: 7nqi
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 2-benzyl-N-cyclopropyl-6-(1-methyl-1H-1,2,3-triazol-4-yl)isonicotinamide
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-UM8 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.603 Å
AuthorsChung, C.W.
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
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9525
Polymers13,4321
Non-polymers5204
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint6 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.016, 52.622, 32.091
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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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-UM8 / 2-benzyl-N-cyclopropyl-6-(1-methyl-1H-1,2,3-triazol-4-yl)isonicotinamide / ~{N}-cyclopropyl-2-(1-methyl-1,2,3-triazol-4-yl)-6-(phenylmethyl)pyridine-4-carboxamide


Mass: 333.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
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: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→72.02 Å / Num. obs: 15827 / % possible obs: 95.4 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.023 / Net I/σ(I): 25.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1868 / CC1/2: 0.817 / % possible all: 79.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.603→27.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 786 -RANDOM
Rwork0.1714 ---
obs0.173 15716 94.5 %-
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.2586 Å20 Å20 Å2
2--1.1978 Å20 Å2
3----1.4564 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.603→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 37 174 1130
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121000HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.021344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d361SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes187HARMONIC5
X-RAY DIFFRACTIONt_it1000HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion115SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1046SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.46
X-RAY DIFFRACTIONt_other_torsion15.21
LS refinement shellResolution: 1.603→1.62 Å
RfactorNum. reflection% reflection
Rfree0.283 24 -
Rwork0.2219 --
obs--67.18 %

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