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- PDB-2pog: Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). P... -

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Basic information

Entry
Database: PDB / ID: 2pog
TitleBenzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure Activity Relationship Studies on the Benzopyran Scaffold.
ComponentsEstrogen receptor
KeywordsLIPID BINDING PROTEIN / nuclear receptor / ligand-binding
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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-WST / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsRichardson, T.I. / Norman, B.H. / Lugar, C.W. / Jones, S.A. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dodge, J.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 2: structure-activity relationship studies on the benzopyran scaffold.
Authors: Richardson, T.I. / Norman, B.H. / Lugar, C.W. / Jones, S.A. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dodge, J.A.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1594
Polymers56,5942
Non-polymers5652
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.584, 99.810, 173.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Estrogen receptor / ER / Estradiol receptor / ER-alpha


Mass: 28297.172 Da / Num. of mol.: 2 / Fragment: ligand binding domain (residues 304-551) / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-WST / (3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-9-OL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M MgCl2, 20 % PEG 4000 and 10% ethylene glycol., VAPOR DIFFUSION, temperature 289K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→25.203 Å / Num. obs: 50399 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.3
Reflection shell

Rmerge(I) obs: 0.012

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.78-1.885.40.63784770721.16396.9
1.88-1.996.11.14249269320.649100
1.99-2.136.11.84009865300.338100
2.13-2.36.243741560760.185100
2.3-2.526.26.33472056300.116100
2.52-2.816.28.73149750960.081100
2.81-3.256.211.72795045310.056100
3.25-3.986.113.22356338430.044100
3.98-5.63614.61802730170.0499.9
5.63-25.25.417.2910916720.03395.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CNXphasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→24.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2220994.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4637 10.1 %RANDOM
Rwork0.233 ---
obs0.235 45835 99.8 %-
all-45835 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.482 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.67 Å20 Å20 Å2
2---0.52 Å20 Å2
3----8.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.84→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 42 118 3707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 1.84→1.96 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 773 10.2 %
Rwork0.316 6795 -
obs-7568 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5lig.par

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