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- PDB-7dpn: Crystal structure of BRD2(BD1)with ligand ZB-BD-224 bound -

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Basic information

Entry
Database: PDB / ID: 7dpn
TitleCrystal structure of BRD2(BD1)with ligand ZB-BD-224 bound
ComponentsBromodomain-containing protein 2
KeywordsANTITUMOR PROTEIN / Antitumor / BET proteins / Bromodomain inhibitor / Epigenetic readers
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 II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-HFU / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79998842375 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 20, 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
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4115
Polymers43,4163
Non-polymers9952
Water3,819212
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)114.784, 55.778, 68.098
Angle α, β, γ (deg.)90.000, 94.245, 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 / O27.1.1 / Really interesting new gene 3 protein


Mass: 14471.866 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-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.: 2 / Source method: obtained synthetically / Formula: C28H23N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25-30% PEG MME 5000, 0.2M ammonium sulfate, 0.1M MES pH 6.7

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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: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.79→46 Å / Num. obs: 39802 / % possible obs: 99.51 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.5503799568 Å2 / CC1/2: 0.941 / CC star: 0.985 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.069 / Rrim(I) all: 0.168 / Rsym value: 0.168 / Net I/σ(I): 99.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.791 / Num. unique obs: 3928 / CC1/2: 0.691 / CC star: 0.904 / Rpim(I) all: 0.985 / Rrim(I) all: 0.861 / Rsym value: 0.791

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Processing

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

2yek


Resolution: 1.79998842375→45.4540515771 Å / SU ML: 0.209194430472 / Cross valid method: THROUGHOUT / σ(F): 1.35505875512 / Phase error: 22.759895183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218792906413 1974 4.96067147488 %
Rwork0.188228271041 37819 -
obs0.189761132575 39793 99.5198199325 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.3003794775 Å2
Refinement stepCycle: LAST / Resolution: 1.79998842375→45.4540515771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 72 214 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006731674305053016
X-RAY DIFFRACTIONf_angle_d0.9039410931134116
X-RAY DIFFRACTIONf_chiral_restr0.0460961591378420
X-RAY DIFFRACTIONf_plane_restr0.00542449894625520
X-RAY DIFFRACTIONf_dihedral_angle_d11.79745464191795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.2881720979041370.2455503173622659X-RAY DIFFRACTION98.3468167429
1.845-1.89490.2742497272441380.2339973335452667X-RAY DIFFRACTION99.9643620813
1.8949-1.95060.2542903935781540.2151325791042707X-RAY DIFFRACTION99.9301432064
1.9506-2.01360.3100178418461520.2135165410842673X-RAY DIFFRACTION99.8233215548
2.0136-2.08560.2716319380851340.1998783698392673X-RAY DIFFRACTION99.5390070922
2.0856-2.16910.1978645951611240.191914818222709X-RAY DIFFRACTION100
2.1691-2.26780.2149707052351210.1942239391832748X-RAY DIFFRACTION100
2.2678-2.38740.252599170381320.2014160821832711X-RAY DIFFRACTION100
2.3874-2.53690.2392879873041240.1958193860892718X-RAY DIFFRACTION99.1625959525
2.5369-2.73280.212133058511340.1922647154622712X-RAY DIFFRACTION100
2.7328-3.00770.2531620116611590.1929063315782685X-RAY DIFFRACTION99.894625922
3.0077-3.44280.2347195981881460.1931636640292701X-RAY DIFFRACTION98.9228630994
3.4428-4.33710.1707248919111640.1619405605742712X-RAY DIFFRACTION99.8957971518
4.3371-450.2127411375571550.1863187506182744X-RAY DIFFRACTION98.0054090602

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