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- PDB-2yly: Sulfonamides as selective Estrogen Receptor beta Agonists. -

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Basic information

Entry
Database: PDB / ID: 2yly
TitleSulfonamides as selective Estrogen Receptor beta Agonists.
ComponentsESTROGEN RECEPTOR BETA
KeywordsRECEPTOR
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-SU4 / Estrogen receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å
AuthorsRoberts, L.R. / Armour, D. / Barker, C. / Bazin, R. / Bess, K. / Brown, A. / Favor, D. / Ellis, D. / MacKenny, M. / Pullen, N. ...Roberts, L.R. / Armour, D. / Barker, C. / Bazin, R. / Bess, K. / Brown, A. / Favor, D. / Ellis, D. / MacKenny, M. / Pullen, N. / Stennett, A. / Strand, L. / Styles, M. / Phillips, C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Sulfonamides as Selective Oestrogen Receptor Beta Agonists.
Authors: Roberts, L.R. / Armor, D. / Barker, C. / Bent, A. / Bess, K. / Brown, A. / Favor, D.A. / Ellis, D. / Irving, S.L. / Mackenny, M. / Phillips, C. / Pullen, N. / Stennett, A. / Strand, L. / Styles, M.
History
DepositionJun 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
B: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1896
Polymers54,3022
Non-polymers8874
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-52.2 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.720, 116.720, 186.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9711, -0.1739, 0.1638), (-0.2146, 0.334, -0.9178), (0.1049, -0.9264, -0.3617)
Vector: -86.52, -45.7, -47.58)

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Components

#1: Protein ESTROGEN RECEPTOR BETA / / ER-BETA / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 2


Mass: 27151.221 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 260-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92731
#2: Chemical ChemComp-SU4 / N-cyclopropyl-4-oxidanyl-N-[(2R)-2-oxidanyl-2-phenyl-propyl]benzenesulfonamide / HYDROXYBENZENESULFONAMIDE


Mass: 347.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO4S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 10980 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 91.65 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 3.2→3.5 Å

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Processing

SoftwareName: BUSTER / Version: 2.9.6 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.9095 / Cor.coef. Fo:Fc free: 0.9013 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.494
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 529 4.82 %RANDOM
Rwork0.2354 ---
obs0.2372 10980 99.76 %-
Displacement parametersBiso mean: 103.44 Å2
Baniso -1Baniso -2Baniso -3
1--9.1489 Å20 Å20 Å2
2---9.1489 Å20 Å2
3---18.2978 Å2
Refine analyzeLuzzati coordinate error obs: 0.813 Å
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 58 0 3538
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013597HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.254858HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1286SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes495HARMONIC5
X-RAY DIFFRACTIONt_it3597HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion24.2
X-RAY DIFFRACTIONt_improper_torsion4HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion456SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4360SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 116 4.52 %
Rwork0.2377 2451 -
all0.2394 2567 -
obs--99.76 %

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