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- PDB-6viy: BRD2_Bromodomain2 complex with pyrrolopyridone compound 27 -

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Basic information

Entry
Database: PDB / ID: 6viy
TitleBRD2_Bromodomain2 complex with pyrrolopyridone compound 27
ComponentsBromodomain-containing protein 2BRD2
KeywordsSIGNALING PROTEIN / bromodomain
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-QYY / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsLongenecker, K.L. / Park, C.H. / Qiu, W.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery ofN-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with ...Title: Discovery ofN-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second Bromodomain.
Authors: Sheppard, G.S. / Wang, L. / Fidanze, S.D. / Hasvold, L.A. / Liu, D. / Pratt, J.K. / Park, C.H. / Longenecker, K. / Qiu, W. / Torrent, M. / Kovar, P.J. / Bui, M. / Faivre, E. / Huang, X. / ...Authors: Sheppard, G.S. / Wang, L. / Fidanze, S.D. / Hasvold, L.A. / Liu, D. / Pratt, J.K. / Park, C.H. / Longenecker, K. / Qiu, W. / Torrent, M. / Kovar, P.J. / Bui, M. / Faivre, E. / Huang, X. / Lin, X. / Wilcox, D. / Zhang, L. / Shen, Y. / Albert, D.H. / Magoc, T.J. / Rajaraman, G. / Kati, W.M. / McDaniel, K.F.
History
DepositionJan 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8763
Polymers26,3682
Non-polymers5081
Water2,324129
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6922
Polymers13,1841
Non-polymers5081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)13,1841
Polymers13,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.990, 68.010, 59.560
Angle α, β, γ (deg.)90.000, 95.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13184.141 Da / Num. of mol.: 2 / Fragment: Bromodomain 2
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-QYY / 4-[2-(2,6-dimethylphenoxy)-5-(ethylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide


Mass: 507.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 25% PEG1500, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.904→44.862 Å / Num. obs: 16430 / % possible obs: 87.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 17.5
Reflection shellResolution: 1.904→1.937 Å / Rmerge(I) obs: 0.733 / Num. unique obs: 463

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (29-NOV-2019)refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uew

5uew


Resolution: 1.904→44.86 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.176
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 757 4.61 %RANDOM
Rwork0.2129 ---
obs0.2148 16430 87.7 %-
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 39.74 Å2 / Biso min: 22.16 Å2
Baniso -1Baniso -2Baniso -3
1--19.49 Å20 Å2-2.2703 Å2
2--9.77 Å20 Å2
3---9.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 1.904→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 36 129 1989
Biso mean--36.44 42.92 -
Num. residues----220
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d668SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it1915HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1708SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1915HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2584HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 1.904→1.94 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.4349 23 5.17 %
Rwork0.3064 422 -
obs--49.95 %

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