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- PDB-6k04: Crystal structure of BRD2(BD2)with ligand BY27 bound -

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Basic information

Entry
Database: PDB / ID: 6k04
TitleCrystal structure of BRD2(BD2)with ligand BY27 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-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
Chem-CQF / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsLu, T. / Lu, W. / Chen, D. / Zhao, Y. / Luo, C.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)81625022 China
National Science Foundation (China)91853205 China
National Science Foundation (China)81821005 China
CitationJournal: Eur.J.Med.Chem. / Year: 2019
Title: Discovery, structural insight, and bioactivities of BY27 as a selective inhibitor of the second bromodomains of BET proteins.
Authors: Chen, D. / Lu, T. / Yan, Z. / Lu, W. / Zhou, F. / Lyu, X. / Xu, B. / Jiang, H. / Chen, K. / Luo, C. / Zhao, Y.
History
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5622
Polymers13,1571
Non-polymers4051
Water2,900161
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)31.835, 52.424, 71.288
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13157.136 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-CQF / (6~{R})-~{N}-(4-chlorophenyl)-1-methyl-8-(1-methylpyrazol-4-yl)-5,6-dihydro-4~{H}-[1,2,4]triazolo[4,3-a][1]benzazepin-6-amine


Mass: 404.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21ClN6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
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: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.251→42.234 Å / Num. obs: 33653 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Net I/σ(I): 34.96
Reflection shellResolution: 1.251→1.296 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 55.29 / Num. unique obs: 3239 / CC1/2: 0.971 / Rpim(I) all: 0.094 / Rrim(I) all: 0.34

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DVV

2dvv


Resolution: 1.251→42.234 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.74
RfactorNum. reflection% reflection
Rfree0.1917 1642 4.88 %
Rwork0.1679 --
obs0.169 33653 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.251→42.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 29 162 1069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006944
X-RAY DIFFRACTIONf_angle_d1.0191278
X-RAY DIFFRACTIONf_dihedral_angle_d21.246346
X-RAY DIFFRACTIONf_chiral_restr0.072126
X-RAY DIFFRACTIONf_plane_restr0.005164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2505-1.28730.23981120.18992555X-RAY DIFFRACTION97
1.2873-1.32890.21231320.17132640X-RAY DIFFRACTION100
1.3289-1.37640.16461100.16652653X-RAY DIFFRACTION100
1.3764-1.43150.17451360.15742634X-RAY DIFFRACTION100
1.4315-1.49670.14491410.15642652X-RAY DIFFRACTION100
1.4967-1.57560.181610.15242603X-RAY DIFFRACTION100
1.5756-1.67430.18341470.15512669X-RAY DIFFRACTION100
1.6743-1.80360.19161420.16062654X-RAY DIFFRACTION100
1.8036-1.98510.17651460.16412668X-RAY DIFFRACTION100
1.9851-2.27230.18771350.16162697X-RAY DIFFRACTION100
2.2723-2.86280.21511290.18042731X-RAY DIFFRACTION100
2.8628-42.25770.19631510.17142855X-RAY DIFFRACTION100

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