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- PDB-7vs1: crystal structure of BRD2-BD2 in complex with purine derivative -

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Basic information

Entry
Database: PDB / ID: 7vs1
Titlecrystal structure of BRD2-BD2 in complex with purine derivative
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/INHIBITOR / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor / TRANSCRIPTION-INHIBITOR COMPLEX
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
3-methyl-7-propyl-purine-2,6-dione / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPadmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. / Mathur, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family.
Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Mathur, S. / Mahalingaswamy, M. / Subramanya, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionOct 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Refinement description / Category: 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)13,7833
Polymers13,4821
Non-polymers3002
Water4,414245
1
A: Bromodomain-containing protein 2
hetero molecules

A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5656
Polymers26,9652
Non-polymers6014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1710 Å2
ΔGint-7 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.539, 71.661, 32.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-845-

HOH

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 13482.371 Da / Num. of mol.: 1 / Mutation: K363S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-7UM / 3-methyl-7-propyl-purine-2,6-dione


Mass: 208.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 2000, 50mM Tris, 50mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 39642 / % possible obs: 97.7 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.78
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 16.78 / Num. unique obs: 1629 / CC1/2: 0.89 / % possible all: 81.9

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XHK

5xhk


Resolution: 1.25→15.37 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1847 1706 5 %
Rwork0.1583 --
obs0.1596 34122 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→15.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 21 245 1203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051044
X-RAY DIFFRACTIONf_angle_d0.8411417
X-RAY DIFFRACTIONf_dihedral_angle_d4.367154
X-RAY DIFFRACTIONf_chiral_restr0.077137
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.290.281370.22282609X-RAY DIFFRACTION97
1.29-1.330.22781380.19082609X-RAY DIFFRACTION98
1.33-1.380.22051390.16222647X-RAY DIFFRACTION99
1.38-1.430.20341410.15132686X-RAY DIFFRACTION100
1.43-1.50.19231400.14852662X-RAY DIFFRACTION100
1.5-1.570.19451420.13752703X-RAY DIFFRACTION100
1.57-1.670.18011420.13712696X-RAY DIFFRACTION100
1.67-1.80.20941440.15322722X-RAY DIFFRACTION100
1.8-1.980.19571420.162702X-RAY DIFFRACTION100
1.98-2.270.1551420.14732710X-RAY DIFFRACTION99
2.27-2.860.15781470.16572772X-RAY DIFFRACTION100
2.86-15.370.18231520.16072898X-RAY DIFFRACTION100

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