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- PDB-7wna: Crystal Structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 7wna
TitleCrystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13120
ComponentsIsoform 4 of Bromodomain-containing protein 2
KeywordsPROTEIN BINDING / BRD2-BD2 / Bromodomain / Inhibitor
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-JGR / DI(HYDROXYETHYL)ETHER / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, J. / Zhang, C. / Xu, H. / Zhuang, X. / Wu, X. / Zhang, Y. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81673357 China
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structure-Based Discovery and Optimization of Furo[3,2- c ]pyridin-4(5 H )-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors.
Authors: Li, J. / Zhang, C. / Xu, H. / Wang, C. / Dong, R. / Shen, H. / Zhuang, X. / Chen, X. / Li, Q. / Lu, J. / Zhang, M. / Wu, X. / Loomes, K.M. / Zhou, Y. / Zhang, Y. / Liu, J. / Xu, Y.
History
DepositionJan 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 4 of Bromodomain-containing protein 2
B: Isoform 4 of Bromodomain-containing protein 2
C: Isoform 4 of Bromodomain-containing protein 2
D: Isoform 4 of Bromodomain-containing protein 2
E: Isoform 4 of Bromodomain-containing protein 2
F: Isoform 4 of Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,03216
Polymers95,8876
Non-polymers4,14510
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.630, 106.630, 87.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Isoform 4 of Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 15981.218 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: BRD2_HUMAN, P25440, sequence from 320-343 are tags. EGDIHMKKGHHHHHHENLYFQGGS
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical
ChemComp-JGR / ~{N}-[4-(4-fluoranyl-2,6-dimethyl-phenoxy)-3-[2-[4-(2-hydroxyethyloxy)-3,5-dimethyl-phenyl]-5-methyl-4-oxidanylidene-furo[3,2-c]pyridin-7-yl]phenyl]ethanesulfonamide


Mass: 634.714 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H35FN2O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 197 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.6→106.63 Å / Num. obs: 30036 / % possible obs: 98.8 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.061 / Rrim(I) all: 0.141 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.725.30.671932136750.6920.3250.7472.3100
9.01-29.574.90.07234867160.9920.0360.08115.692.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6J

6e6j


Resolution: 2.6→106.63 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 12.617 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1562 5.2 %RANDOM
Rwork0.2085 ---
obs0.2116 28466 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.29 Å2 / Biso mean: 56.596 Å2 / Biso min: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å2-0 Å2-0 Å2
2--1.54 Å2-0 Å2
3----3.09 Å2
Refinement stepCycle: final / Resolution: 2.6→106.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 292 60 5721
Biso mean--48.52 34.72 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025838
X-RAY DIFFRACTIONr_bond_other_d0.0020.025308
X-RAY DIFFRACTIONr_angle_refined_deg1.6942.0097899
X-RAY DIFFRACTIONr_angle_other_deg1.0293.01112286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96123.428283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09715988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.141536
X-RAY DIFFRACTIONr_chiral_restr0.0860.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216341
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021237
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 112 -
Rwork0.32 2095 -
all-2207 -
obs--99.59 %

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