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- PDB-7dpo: Crystal Structure of BRD2(BD2)with Ligand ZB-BD-224 bound -

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Basic information

Entry
Database: PDB / ID: 7dpo
TitleCrystal Structure of BRD2(BD2)with Ligand ZB-BD-224 bound
ComponentsBromodomain-containing protein 2BRD2
KeywordsANTITUMOR PROTEIN / Antitumor / BET proteins / Bromodomain inhibitor / Epigenetic readers
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-HFU / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29994028999 Å
AuthorsLi, Z. / Lu, T. / Chen, P. / Luo, C. / Zhou, B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853205 China
National Natural Science Foundation of China (NSFC)81625022 China
National Natural Science Foundation of China (NSFC)81821005 China
CitationJournal: To Be Published
Title: Structure Base Design of A new chemotype of Four-Cycle Compounds as Bromodomain and Extra-Terminal (BET) Inhibitors with The Second Bromodomain Bias and Highly Anti-inflammatory Potency
Authors: Li, Z. / Lu, T. / Chen, P. / Luo, C. / Zgou, B.
History
DepositionDec 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: 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: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6822
Polymers13,1841
Non-polymers4981
Water55831
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.736, 35.541, 47.204
Angle α, β, γ (deg.)90.000, 117.627, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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.: 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-HFU / 5-(1-naphthoyl)-11-methyl-8-((methylsulfonyl)methyl)-4,5-dihydro-2,3a1,5-triazadibenzo[cd,h]azulen-1(2H)-one


Mass: 497.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H23N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium sulfate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→42 Å / Num. obs: 5522 / % possible obs: 98.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 42.1319108441 Å2 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.067 / Rrim(I) all: 0.166 / Net I/σ(I): 98.3
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 538 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.221 / Rrim(I) all: 0.474

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVV

2dvv


Resolution: 2.29994028999→41.8220433854 Å / SU ML: 0.246562437757 / Cross valid method: FREE R-VALUE / σ(F): 1.41696569125 / Phase error: 16.6463442538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241899518161 280 5.07430228344 %
Rwork0.200194913028 5238 -
obs0.202513494492 5518 98.1326693936 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1096440118 Å2
Refinement stepCycle: LAST / Resolution: 2.29994028999→41.8220433854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 36 32 974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913196726336971
X-RAY DIFFRACTIONf_angle_d1.117917600591315
X-RAY DIFFRACTIONf_chiral_restr0.0444877805887126
X-RAY DIFFRACTIONf_plane_restr0.00700319076067167
X-RAY DIFFRACTIONf_dihedral_angle_d12.4223983584569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.89760.2977549132871230.1901933844992596X-RAY DIFFRACTION97.9114151963
2.8976-410.2298724156931570.2033147517052642X-RAY DIFFRACTION98.3485593816

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