2QTU | pdb_00002qtu

Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand

PDB DOI: https://doi.org/10.2210/pdb2QTU/pdb

Classification: transcription regulator
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-02 Released: 2007-10-30
Deposition Author(s): Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.279 (Depositor), 0.284 (DCC)
R-Value Work:
0.264 (Depositor), 0.262 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 5: Combined A- and C-ring structure-activity relationship studies.

Richardson, T.I., Dodge, J.A., Wang, Y., Durbin, J.D., Krishnan, V., Norman, B.H.

(2007) Bioorg Med Chem Lett 17: 5563-5566

PubMed: 17804226 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.08.009
Primary Citation Related Structures:
2QTU

PubMed Abstract:
Benzopyrans are selective estrogen receptor (ER) beta agonists (SERBAs), which bind the ER subtypes alpha and beta in opposite orientations. Here we describe the synthesis of a late stage intermediate that allowed us to combine A-ring and C-ring modifications and carry out simultaneous SAR studies at both positions. Modification of both positions proved additive, maintaining affinity and improving ERbeta selectivity up to 83-fold. An X-ray cocrystal structure confirms the previously observed binding mode in ERbeta.

Organizational Affiliation

Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. t_richardson@lilly.com

Macromolecule Content

Total Structure Weight: 59.18 kDa
Atom Count: 3,514
Modeled Residue Count: 441
Deposited Residue Count: 514
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	257	Homo sapiens	Mutation(s): 0 Gene Names: ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731 Go to UniProtKB: Q92731
PHAROS: Q92731 GTEx: ENSG00000140009
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92731
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3AS Query on 3AS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol C₂₀ H₂₀ F₂ O₄ GPFRMIHXGMVMGF-BZSNNMDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.279 (Depositor), 0.284 (DCC)
R-Value Work: 0.264 (Depositor), 0.262 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.798	α = 90
b = 63.798	β = 90
c = 249.616	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-10-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations