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- PDB-7wn5: Crystal Structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 7wn5
TitleCrystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13142
ComponentsIsoform 4 of Bromodomain-containing protein 2
KeywordsPROTEIN BINDING / BRD2-BD2 / Bromodomain / Inhibitor
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-JGL / : / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,36510
Polymers31,9622
Non-polymers1,4028
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint2 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.979, 63.610, 72.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 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-JGL / ~{N}-[4-[2,4-bis(fluoranyl)phenoxy]-3-[2-(1~{H}-imidazol-5-yl)-5-methyl-4-oxidanylidene-furo[3,2-c]pyridin-7-yl]phenyl]ethanesulfonamide


Mass: 526.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H20F2N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.83 Å3/Da / Density % sol: 32.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 197 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→47.71 Å / Num. obs: 26476 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.04 / Rrim(I) all: 0.125 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1 / Redundancy: 9.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.730.7331296313670.960.2460.7742.599.7
9-41.630.06621252230.9950.0230.0715.599.5

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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: 4QEW

4qew


Resolution: 1.7→47.71 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.195 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1278 4.9 %RANDOM
Rwork0.2299 ---
obs0.2317 24900 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.17 Å2 / Biso mean: 18.215 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--1.15 Å2-0 Å2
3----1.93 Å2
Refinement stepCycle: final / Resolution: 1.7→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 95 158 2184
Biso mean--23.57 26.51 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022111
X-RAY DIFFRACTIONr_bond_other_d0.0020.021892
X-RAY DIFFRACTIONr_angle_refined_deg1.7282.0012851
X-RAY DIFFRACTIONr_angle_other_deg0.973.0064398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04123.846104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9141512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212334
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 82 -
Rwork0.418 1815 -
all-1897 -
obs--99.79 %

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