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- PDB-6mo8: N-terminal bromodomain of human BRD2 in complex with 4,4'-(quinol... -

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Basic information

Entry
Database: PDB / ID: 6mo8
TitleN-terminal bromodomain of human BRD2 in complex with 4,4'-(quinoline-5,7-diyl)bis(3,5-dimethylisoxazole) inhibitor
ComponentsBromodomain-containing protein 2
Keywordstranscription/transcription inhibitor / inhibitor / epigenetic reader / bromodomain / transcription-transcription inhibitor complex
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 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
5,7-bis(3,5-dimethyl-1,2-oxazol-4-yl)quinoline / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLansdon, E.B. / Newby, Z.E.R.
CitationJournal: Bioorg. Med. Chem. / Year: 2019
Title: Structure-guided discovery of a novel, potent, and orally bioavailable 3,5-dimethylisoxazole aryl-benzimidazole BET bromodomain inhibitor.
Authors: Sperandio, D. / Aktoudianakis, V. / Babaoglu, K. / Chen, X. / Elbel, K. / Chin, G. / Corkey, B. / Du, J. / Jiang, B. / Kobayashi, T. / Mackman, R. / Martinez, R. / Yang, H. / Zablocki, J. / ...Authors: Sperandio, D. / Aktoudianakis, V. / Babaoglu, K. / Chen, X. / Elbel, K. / Chin, G. / Corkey, B. / Du, J. / Jiang, B. / Kobayashi, T. / Mackman, R. / Martinez, R. / Yang, H. / Zablocki, J. / Kusam, S. / Jordan, K. / Webb, H. / Bates, J.G. / Lad, L. / Mish, M. / Niedziela-Majka, A. / Metobo, S. / Sapre, A. / Hung, M. / Jin, D. / Fung, W. / Kan, E. / Eisenberg, G. / Larson, N. / Newby, Z.E.R. / Lansdon, E. / Tay, C. / Neve, R.M. / Shevick, S.L. / Breckenridge, D.G.
History
DepositionOct 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,8037
Polymers44,7493
Non-polymers1,0544
Water4,576254
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5553
Polymers14,9161
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3323
Polymers14,9161
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bromodomain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)14,9161
Polymers14,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.221, 55.773, 67.676
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-251-

HOH

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Components

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


Mass: 14916.436 Da / Num. of mol.: 3
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-JWD / 5,7-bis(3,5-dimethyl-1,2-oxazol-4-yl)quinoline


Mass: 319.357 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H17N3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 29% PEG 3350 225 mM ammonium sulfate 100mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40307 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 22.2
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.286 / Num. unique obs: 4015 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.388 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2233 1954 4.94 %
Rwork0.186 --
obs0.1878 39528 96.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 40.184 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2836 Å20 Å2-2.5057 Å2
2--0.5204 Å20 Å2
3----2.804 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 77 254 3069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063019
X-RAY DIFFRACTIONf_angle_d0.924116
X-RAY DIFFRACTIONf_dihedral_angle_d15.1531145
X-RAY DIFFRACTIONf_chiral_restr0.063420
X-RAY DIFFRACTIONf_plane_restr0.004521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7904-1.83520.31331070.262339X-RAY DIFFRACTION85
1.8352-1.88480.25531360.22412596X-RAY DIFFRACTION94
1.8848-1.94030.22881440.20692659X-RAY DIFFRACTION96
1.9403-2.00290.28291330.19462666X-RAY DIFFRACTION96
2.0029-2.07450.23491430.19352684X-RAY DIFFRACTION98
2.0745-2.15760.24451450.1862700X-RAY DIFFRACTION98
2.1576-2.25570.23351280.18142761X-RAY DIFFRACTION99
2.2557-2.37470.21321590.18642712X-RAY DIFFRACTION99
2.3747-2.52340.19421370.18562742X-RAY DIFFRACTION99
2.5234-2.71820.21311480.17982740X-RAY DIFFRACTION99
2.7182-2.99170.22581450.18922736X-RAY DIFFRACTION99
2.9917-3.42450.25781410.19172751X-RAY DIFFRACTION98
3.4245-4.31380.19041460.16892728X-RAY DIFFRACTION98
4.3138-42.40.22331420.18472760X-RAY DIFFRACTION96

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