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- PDB-8ev1: Dual Modulators -

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Basic information

Entry
Database: PDB / ID: 8ev1
TitleDual Modulators
Components
  • Estrogen Receptor
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsDNA BINDING PROTEIN / ER-alpha / ligand complex / carbonic anhydrase
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-WVR / Chem-WVW / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsTinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Rangarajan, E.S. / Christodoulou, M. ...Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Rangarajan, E.S. / Christodoulou, M. / Passarella, D. / Supuran, C. / Nettles, K.W. / Rastelli, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors.
Authors: Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Erumbi, R. / Christodoulou, M.S. / Passarella, D. / Supuran, C.T. / ...Authors: Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Erumbi, R. / Christodoulou, M.S. / Passarella, D. / Supuran, C.T. / Nettles, K.W. / Rastelli, G.
History
DepositionOct 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Estrogen Receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9637
Polymers61,9304
Non-polymers1,0333
Water2,324129
1
A: Estrogen Receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6254
Polymers30,9362
Non-polymers6892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area11510 Å2
MethodPISA
2
B: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3383
Polymers30,9942
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-8 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.055, 82.633, 58.553
Angle α, β, γ (deg.)90.000, 110.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Estrogen Receptor


Mass: 29356.586 Da / Num. of mol.: 1 / Fragment: Ligand binding domain / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29413.637 Da / Num. of mol.: 1 / Fragment: Ligand binding domain / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596

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Non-polymers , 3 types, 132 molecules

#4: Chemical ChemComp-WVW / (3aS,4R,9bR)-4-(4-hydroxyphenyl)-2,3,3a,4,5,9b-hexahydro-1H-cyclopenta[c]quinoline-8-sulfonamide


Mass: 344.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-WVR / (3aR,4S,9bS)-4-(4-hydroxyphenyl)-2,3,3a,4,5,9b-hexahydro-1H-cyclopenta[c]quinoline-8-sulfonamide


Mass: 344.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 20-25% PEG 3350, 200 mM MgCl2, 200 mM NaCl, 0.1 M Hepes pH 7
PH range: 6.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.828→50.54 Å / Num. obs: 27680 / % possible obs: 92.6 % / Redundancy: 7.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Net I/σ(I): 12
Reflection shellResolution: 1.828→2.068 Å / Num. unique obs: 1385 / CC1/2: 0.513

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qzo

2qzo


Resolution: 1.83→50.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.527 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1383 5 %RANDOM
Rwork0.1761 ---
obs0.1785 26302 64.78 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 223.65 Å2 / Biso mean: 48.005 Å2 / Biso min: 9.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.18 Å2
2--0.31 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.83→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 72 129 4089
Biso mean--91.73 39.92 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0184106
X-RAY DIFFRACTIONr_bond_other_d0.0020.023965
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9465554
X-RAY DIFFRACTIONr_angle_other_deg1.0572.9339179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07324.226168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82715772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.051522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.873 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.38 3 -
Rwork0.398 38 -
obs--1.31 %
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)
15.92974.3056-0.21687.61810.27533.02370.2275-0.36770.20130.3705-0.2140.336-0.05110.0668-0.01350.05280.0173-0.00250.0726-0.02990.03435.63916.21433.384
23.6703-0.3686-0.91074.1833-1.42723.3969-0.03910.0142-0.1793-0.1470.02920.10320.2051-0.17390.00990.014-0.0089-0.00360.0162-0.00250.0211.05112.17125.705
317.28535.69245.3196.38161.85815.14820.052-0.0395-0.4701-0.1843-0.1227-0.09860.4358-0.00020.07070.1170.02650.05540.023-0.01710.11259.9512.47420.26
44.85040.583-0.01942.2169-0.09473.88790.0468-0.03150.2209-0.0991-0.07270.0207-0.1940.20310.02590.0178-0.0092-0.00020.02130.00320.020514.01619.4119.868
59.539-0.08951.70414.57510.689410.1220.07720.3821-0.759-0.5322-0.1140.01060.274-0.54950.03680.0886-0.0225-0.02940.2309-0.02770.2317-10.78113.57718.808
64.5382-0.22233.90282.5723-1.04058.3786-0.0891-0.25460.0244-0.1671-0.0921-0.20870.3020.55710.18110.13790.02350.09090.21240.00390.071124.34315.565-5.385
72.4190.53740.28682.691-0.62917.1662-0.22130.1293-0.1840.02390.023-0.0270.7642-0.08080.19830.20250.01810.06660.02870.00030.041114.9039.818-4.397
84.05580.9466-4.28666.3842.133814.1063-0.1890.57170.5786-0.40770.04150.3118-1.1052-0.30430.14750.31980.0234-0.1160.16640.11330.153810.9627.779-8.885
910.23316.68556.253215.2804-2.057.2736-0.0324-0.25180.2336-0.27450.09640.47220.1485-0.3207-0.0640.46980.20990.04310.5720.03570.5496-2.5225.524-5.824
1018.44952.27492.36264.3362-0.84533.8976-0.0564-0.11030.51760.0602-0.04020.2675-0.3941-0.36310.09650.21060.0873-0.00150.07930.01680.07358.67326.7222.116
113.45311.04530.92159.11-1.85874.2337-0.0631-0.0268-0.23460.117-0.1480.03090.36810.28270.21110.09880.04480.05390.13550.0130.048720.93310.6747.172
124.37550.38590.65742.8242-0.22435.3699-0.12510.0554-0.1391-0.2698-0.0423-0.13620.11380.39270.16740.03950.01580.02790.07680.030.027219.7616.1089.082
1317.6507-1.6643-3.68278.26062.60932.6187-0.24020.07580.01520.36320.06230.41330.2856-0.23870.1780.3881-0.1330.05150.3589-0.02010.30581.6025.889-6.225
149.63923.6691-0.808112.21682.99363.8455-0.0308-0.11630.2942-0.16680.11560.4236-0.2487-0.1217-0.08480.11160.0485-0.01430.06330.00410.201-8.36227.59526.241
1512.914-0.40251.65110.66910.32170.4472-0.04970.5133-0.81980.22610.2147-0.03290.20580.1856-0.1650.43970.02490.00890.1144-0.05110.275715.416-2.293-8.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 338
2X-RAY DIFFRACTION2A339 - 421
3X-RAY DIFFRACTION3A422 - 437
4X-RAY DIFFRACTION4A438 - 530
5X-RAY DIFFRACTION5A531 - 547
6X-RAY DIFFRACTION6B307 - 338
7X-RAY DIFFRACTION7B339 - 394
8X-RAY DIFFRACTION8B395 - 411
9X-RAY DIFFRACTION9B412 - 421
10X-RAY DIFFRACTION10B422 - 437
11X-RAY DIFFRACTION11B438 - 469
12X-RAY DIFFRACTION12B470 - 530
13X-RAY DIFFRACTION13B531 - 548
14X-RAY DIFFRACTION14C568 - 576
15X-RAY DIFFRACTION15D568 - 576

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