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- PDB-5ak2: Oxyphenylpropenoic acids as Oral Selective Estrogen Receptor Down... -

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Basic information

Entry
Database: PDB / ID: 5ak2
TitleOxyphenylpropenoic acids as Oral Selective Estrogen Receptor Down- Regulators.
ComponentsESTROGEN RECEPTOR
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / 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 / Double treble clef zinc finger, C4 type / 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-85Z / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsDegorce, S. / Bailey, A. / Callis, R. / De Savi, C. / Ducray, R. / Lamot, P. / MacFaul, P. / Maudet, M. / Norman, R.A. / Scott, J.S. / Phillips, C.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Investigation of (E)-3-[4-(2-Oxo-3-Aryl-Chromen-4-Yl)Oxyphenyl]Acrylic Acids as Oral Selective Estrogen Receptor Down-Regulators.
Authors: Degorce, S.L. / Bailey, A. / Callis, R. / De Savi, C. / Ducray, R. / Lamont, G. / Macfaul, P. / Maudet, M. / Martin, S. / Morgentin, R. / Norman, R.A. / Peru, A. / Pink, J.H. / Ple, P.A. / ...Authors: Degorce, S.L. / Bailey, A. / Callis, R. / De Savi, C. / Ducray, R. / Lamont, G. / Macfaul, P. / Maudet, M. / Martin, S. / Morgentin, R. / Norman, R.A. / Peru, A. / Pink, J.H. / Ple, P.A. / Roberts, B. / Scott, J.S.
History
DepositionFeb 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3May 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,0244
Polymers61,1632
Non-polymers8612
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-12.8 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.070, 51.290, 83.310
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ESTROGEN RECEPTOR / ER / ER-ALPHA / ESTRADIOL RECEPTOR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1 / ESTROGEN RECEPTOR ALPHA


Mass: 30581.586 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 307-554 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-85Z / (E)-3-[4-[[3-(4-fluoranyl-2-methyl-phenyl)-7-oxidanyl-2-oxidanylidene-chromen-4-yl]methyl]phenyl]prop-2-enoic acid


Mass: 430.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H19FO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.62 % / Description: NONE
Crystal growDetails: OF 0.1 M PCTP, PH 6.5 (0.04 M SODIUM PROPIONATE, 0.02 M SODIUM CACODYLATE, 0.04 M BIS-TRIS PROPANE), 22% PEG3350, 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Type: DIAMOND / Wavelength: 0.917
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.19→46.17 Å / Num. obs: 22868 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0107 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→46.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.172 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26226 1172 5.1 %RANDOM
Rwork0.21191 ---
obs0.21449 21696 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.349 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20.18 Å2
2---0.05 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.19→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 64 142 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193515
X-RAY DIFFRACTIONr_bond_other_d0.0060.023394
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9564757
X-RAY DIFFRACTIONr_angle_other_deg1.02437760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96123.897136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11915621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7291518
X-RAY DIFFRACTIONr_chiral_restr0.090.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02761
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1022.9131744
X-RAY DIFFRACTIONr_mcbond_other1.1012.911743
X-RAY DIFFRACTIONr_mcangle_it1.8094.3462166
X-RAY DIFFRACTIONr_mcangle_other1.8094.3492167
X-RAY DIFFRACTIONr_scbond_it1.2432.9491771
X-RAY DIFFRACTIONr_scbond_other1.2462.9481734
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9664.3852541
X-RAY DIFFRACTIONr_long_range_B_refined4.15822.7934121
X-RAY DIFFRACTIONr_long_range_B_other3.97822.573987
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.188→2.245 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 98 -
Rwork0.263 1593 -
obs--97.41 %
Refinement TLS params.Method: refined / Origin x: 40.8252 Å / Origin y: 0.2046 Å / Origin z: 22.7633 Å
111213212223313233
T0.0221 Å20.0114 Å20.0015 Å2-0.045 Å20.0062 Å2--0.0017 Å2
L0.6879 °2-0.2566 °2-0.0399 °2-0.0962 °20.0066 °2--0.248 °2
S0.0115 Å °0.0317 Å °0.021 Å °-0.0033 Å °-0.0128 Å °-0.0077 Å °0.0126 Å °0.0347 Å °0.0013 Å °

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