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- PDB-7enz: Crystal structure of Phenanthredinone moiety in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 7enz
TitleCrystal structure of Phenanthredinone moiety in complex with the second bromodomain of BRD2 (BRD2-BD2).
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor
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
phenanthridin-6(5H)-one / TRIETHYLENE GLYCOL / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPadmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structural investigation of a pyrano-1,3-oxazine derivative and the phenanthridinone core moiety against BRD2 bromodomains.
Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Padmanabhan, B.
#1: Journal: J Biomol Struct Dyn / Year: 2018
Title: Insights into the crystal structure of BRD2-BD2 - phenanthridinone complex and theoretical studies on phenanthridinone analogs.
Authors: Mathur, S. / Deshmukh, P. / Tripathi, S. / Marimuthu, P. / Padmanabhan, B.
#2: Journal: Biochem.J. / Year: 2020
Title: Novel pyrano 1,3 oxazine based ligand inhibits the epigenetic reader hBRD2 in glioblastoma.
Authors: Deshmukh, P. / Mathur, S. / Gangadharan, G. / Krishnappa, G. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionApr 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 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)13,7523
Polymers13,4061
Non-polymers3452
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint5 kcal/mol
Surface area7060 Å2
Unit cell
Length a, b, c (Å)32.023, 52.672, 71.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-936-

HOH

21A-1016-

HOH

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Components

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


Mass: 13406.319 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 348-455
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-LDR / phenanthridin-6(5H)-one


Mass: 195.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM Tris pH 7.5, 50 mM NaCl, 25% PEG MME 2000

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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: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.7→14.1 Å / Num. obs: 13875 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.6
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 700 / CC1/2: 0.54

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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: 1.7→14.1 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 650 4.7 %
Rwork0.1886 --
obs0.1905 13834 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→14.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 25 218 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071030
X-RAY DIFFRACTIONf_angle_d0.8131392
X-RAY DIFFRACTIONf_dihedral_angle_d4.55159
X-RAY DIFFRACTIONf_chiral_restr0.048136
X-RAY DIFFRACTIONf_plane_restr0.005202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.830.26691110.19672592X-RAY DIFFRACTION100
1.83-2.010.28971260.24592611X-RAY DIFFRACTION100
2.02-2.310.24691340.19392607X-RAY DIFFRACTION100
2.31-2.90.24021400.18892630X-RAY DIFFRACTION100

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