Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.04 kDa 
• Atom Count: 4070 
• Modelled Residue Count: 482 
• Deposited Residue Count: 542 
• Unique protein chains: 2

5KD9

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-trifluoroethyl 4-chlorobenzyl OBHS-N derivative

• PDB DOI: 10.2210/pdb5KD9/pdb
• Entry: 5KD9 supersedes: 5BQ4

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-06-07 Released: 2016-11-16 
• Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Bruno, N.E., Dharmarajan, V., Goswami, D., Kastrati, I., Novick, S., Nowak, J., Zhou, H.B., Boonmuen, N., Zhao, Y., Min, J., Frasor, J., Katzenellenbogen, B.S., Griffin, P.R., Katzenellenbogen, J.A., Nettles, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Full antagonism of the estrogen receptor without a prototypical ligand side chain.

Srinivasan, S., Nwachukwu, J.C., Bruno, N.E., Dharmarajan, V., Goswami, D., Kastrati, I., Novick, S., Nowak, J., Cavett, V., Zhou, H.B., Boonmuen, N., Zhao, Y., Min, J., Frasor, J., Katzenellenbogen, B.S., Griffin, P.R., Katzenellenbogen, J.A., Nettles, K.W.

(2017) Nat Chem Biol 13: 111-118

• PubMed: 27870835 
• DOI: 10.1038/nchembio.2236
• Primary Citation of Related Structures:  
  5KCC, 5KCD, 5KCE, 5KCF, 5KCT, 5KCU, 5KCW, 5KD9


• PubMed Abstract: 
  

Resistance to endocrine therapies remains a major clinical problem for the treatment of estrogen receptor-α (ERα)-positive breast cancer. On-target side effects limit therapeutic compliance and use for chemoprevention, highlighting an unmet need for new therapies. Here we present a full-antagonist ligand series lacking the prototypical ligand side chain that has been universally used to engender antagonism of ERα through poorly understood structural mechanisms. A series of crystal structures and phenotypic assays reveal a structure-based design strategy with separate design elements for antagonism and degradation of the receptor, and access to a structurally distinct space for further improvements in ligand design. Understanding structural rules that guide ligands to produce diverse ERα-mediated phenotypes has broad implications for the treatment of breast cancer and other estrogen-sensitive aspects of human health including bone homeostasis, energy metabolism, and autoimmunity.

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Organizational Affiliation: 

Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	257	Homo sapiens	Mutation(s): 1  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NCOA2	C, D	14	Homo sapiens	Mutation(s): 0  Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OBT	E [auth A], F [auth B]	(1S,2R,4S)-N-(4-chlorophenyl)-5,6-bis(4-hydroxyphenyl)-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide C26 H21 Cl F3 N O5 S IMJVXTIQVJFSBH-SGIRGMQISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OBT	Binding MOAD:  5KD9	IC50: 930 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.213 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.951	α = 90
b = 81.654	β = 110.97
c = 58.795	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-06-07 
• Released Date: 2016-11-16 
Deposition Author(s): Nwachukwu, J.C., Srinivasan, S., Bruno, N.E., Dharmarajan, V., Goswami, D., Kastrati, I., Novick, S., Nowak, J., Zhou, H.B., Boonmuen, N., Zhao, Y., Min, J., Frasor, J., Katzenellenbogen, B.S., Griffin, P.R., Katzenellenbogen, J.A., Nettles, K.W.
• This entry supersedes: 5BQ4

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Database references
• Version 1.2: 2016-12-28
  Changes: Database references
• Version 1.3: 2020-02-26
  Changes: Derived calculations