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- PDB-7qvl: OESTROGEN RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH COMPOUND 38 -

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Basic information

Entry
Database: PDB / ID: 7qvl
TitleOESTROGEN RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH COMPOUND 38
ComponentsEstrogen receptor
KeywordsGENE REGULATION / OESTROGEN RECEPTOR
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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / chromatin / regulation of DNA-templated transcription / 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 / membrane / identical protein binding / 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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related 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
Similarity search - Domain/homology
Chem-GZI / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBreed, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a Potent and Orally Bioavailable Zwitterionic Series of Selective Estrogen Receptor Degrader-Antagonists.
Authors: Scott, J.S. / Stead, D. / Barlaam, B. / Breed, J. / Carbajo, R.J. / Chiarparin, E. / Cureton, N. / Davey, P.R.J. / Fisher, D.I. / Gangl, E.T. / Grebe, T. / Greenwood, R.D. / Hande, S. / ...Authors: Scott, J.S. / Stead, D. / Barlaam, B. / Breed, J. / Carbajo, R.J. / Chiarparin, E. / Cureton, N. / Davey, P.R.J. / Fisher, D.I. / Gangl, E.T. / Grebe, T. / Greenwood, R.D. / Hande, S. / Hatoum-Mokdad, H. / Hughes, S.J. / Hunt, T.A. / Johnson, T. / Kavanagh, S.L. / Klinowska, T.C.M. / Larner, C.J.B. / Lawson, M. / Lister, A.S. / Longmire, D. / Marden, S. / McGuire, T.M. / McMillan, C. / McMurray, L. / Morrow, C.J. / Nissink, J.W.M. / Moss, T.A. / O'Donovan, D.H. / Polanski, R. / Stokes, S. / Thakur, K. / Trueman, D. / Truman, C. / Tucker, M.J. / Wang, H. / Whalley, N. / Wu, D. / Wu, Y. / Yang, B. / Yang, W.
History
DepositionJan 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: 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: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3124
Polymers57,3112
Non-polymers1,0012
Water3,243180
1
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1562
Polymers28,6561
Non-polymers5011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1562
Polymers28,6561
Non-polymers5011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.330, 52.390, 85.990
Angle α, β, γ (deg.)90.000, 93.010, 90.000
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


Mass: 28655.521 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-GZI / (2~{R})-3-[(1~{R},3~{R})-1-[5-fluoranyl-2-[2-(3-fluoranylpropylamino)ethoxy]-3-methyl-pyridin-4-yl]-3-methyl-1,3,4,9-tetrahydropyrido[3,4-b]indol-2-yl]-2-methyl-propanoic acid


Mass: 500.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H34F2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97627 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.9→46.98 Å / Num. obs: 36588 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.11 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Rrim(I) all: 0.097 / Net I/σ(I): 8.8 / Num. measured all: 118318 / Scaling rejects: 58
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Rmerge(I) obs: 2.882 / Num. unique obs: 2502 / CC1/2: 0.504 / Rpim(I) all: 1.954 / Rrim(I) all: 3.496 / % possible all: 91.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
AMoREphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SUO

6suo


Resolution: 1.9→46.98 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0.022 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1659 4.72 %RANDOM
Rwork0.205 ---
obs0.207 35146 93.7 %-
Displacement parametersBiso max: 146.5 Å2 / Biso mean: 48.07 Å2 / Biso min: 23.19 Å2
Baniso -1Baniso -2Baniso -3
1-4.1098 Å20 Å20.2216 Å2
2---4.3706 Å20 Å2
3---0.2608 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.9→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 72 180 3698
Biso mean--40.02 51.53 -
Num. residues----456
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1251SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes533HARMONIC5
X-RAY DIFFRACTIONt_it3656HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
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_contact4376SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3656HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4972HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion16.48
LS refinement shellResolution: 1.9→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.266 60 4.47 %
Rwork0.242 1283 -
all0.243 1343 -
obs--44.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4045-0.8545-0.78781.90520.26751.453-0.0565-0.2137-0.16480.01550.0241-0.05690.01960.25840.0325-0.09910.06230.0078-0.07840.0671-0.177720.2866-5.714922.9957
23.09840.1970.01151.0566-0.03911.9339-0.0076-0.055-0.03740.00010.09270.0808-0.1364-0.2112-0.0851-0.03470.06590.0225-0.120.0376-0.1305-4.09076.342423.3142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A303 - 552
2X-RAY DIFFRACTION2{ B|* }B308 - 546

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