5AK2

Oxyphenylpropenoic acids as Oral Selective Estrogen Receptor Down- Regulators.

PDB DOI: https://doi.org/10.2210/pdb5AK2/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-02-27 Released: 2015-04-22
Deposition Author(s): Degorce, S., Bailey, A., Callis, R., De Savi, C., Ducray, R., Lamot, P., MacFaul, P., Maudet, M., Norman, R.A., Scott, J.S., Phillips, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Investigation of (E)-3-[4-(2-Oxo-3-Aryl-Chromen-4-Yl)Oxyphenyl]Acrylic Acids as Oral Selective Estrogen Receptor Down-Regulators.

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.

(2015) J Med Chem 58: 3522

PubMed: 25790336 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5b00066
Primary Citation of Related Structures:
5AK2

PubMed Abstract:
A novel estrogen receptor down-regulator, 7-hydroxycoumarin (5, SS5020), has been reported with antitumor effects against chemically induced mammary tumors. Here, we report on our own investigation of 7-hydroxycoumarins as potential selective estrogen receptor down-regulators, which led us to the discovery of potent down-regulating antagonists, such as 33. Subsequent optimization and removal of the 7-hydroxy group led to coumarin 59, which had increased potency and improved rat bioavailability relative to SS5020.

Organizational Affiliation

†Oncology Innovative Medicines Unit, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, United Kingdom.

Macromolecule Content

Total Structure Weight: 62.02 kDa
Atom Count: 3,593
Modelled Residue Count: 438
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR	A, B	268	Homo sapiens	Mutation(s): 4
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372 Go to UniProtKB: P03372
PHAROS: P03372 GTEx: ENSG00000091831
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
85Z Query on 85Z Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(E)-3-[4-[[3-(4-fluoranyl-2-methyl-phenyl)-7-oxidanyl-2-oxidanylidene-chromen-4-yl]methyl]phenyl]prop-2-enoic acid C₂₆ H₁₉ F O₅ OESYVSZPQCBFQS-IZZDOVSWSA-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: 2.19 Å
R-Value Free: 0.262
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.07	α = 90
b = 51.29	β = 91.45
c = 83.31	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2015-05-13
Changes: Database references
Version 1.2: 2018-04-25
Changes: Data collection
Version 1.3: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other