5G3J

Discovery of New Selective Glucocorticoid Receptor Agonist Leads

• PDB DOI:  https://doi.org/10.2210/pdb5G3J/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2016-04-27 Released: 2017-02-15 
• Deposition Author(s): Berger, M., Edman, K., Wissler, L., Neuhaus, R., Rehwinkel, H., Schacke, H., Jaroch, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Literature

Discovery of New Selective Glucocorticoid Receptor Agonist Leads.

Berger, M., Rehwinkel, H., Schmees, N., Schacke, H., Edman, K., Wissler, L., Reichel, A., Jaroch, S.

(2017) Bioorg Med Chem Lett 27: 437

• PubMed: 28043796 
• DOI: https://doi.org/10.1016/j.bmcl.2016.12.047
• Primary Citation of Related Structures:  
  5G3J


• PubMed Abstract: 
  

We report on the discovery of two new lead series for the development of glucocorticoid receptor agonists. Firstly, the discovery of tetrahydronaphthalenes led to metabolically stable and dissociated compounds. Their binding mode to the glucocorticoid receptor could be elucidated through an X-ray structure. Closer inspection into the reaction path and analyses of side products revealed a new amino alcohol series also addressing the glucocorticoid receptor and demonstrating strong anti-inflammatory activity in vitro.

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Organizational Affiliation: 

Global External Innovation & Alliances, Candidate Generation & External Innovation, Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 35.03 kDa 
• Atom Count: 2,279 
• Modelled Residue Count: 261 
• Deposited Residue Count: 294 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOCORTICOID RECEPTOR	A	280	Homo sapiens	Mutation(s): 4  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR RECEPTOR COACTIVATOR 2	B	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	C [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
E7T	E [auth A]	5-[[(1S,2R,4R)-4-ethyl-6,7-bis(fluoranyl)-2,5-bis(oxidanyl)-2-(trifluoromethyl)-3,4-dihydro-1H-naphthalen-1-yl]amino]-1H-quinolin-2-one C22 H19 F5 N2 O3 VZPLUSXTJULLCS-SYQZRHMFSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E7T	Binding MOAD:  5G3J	IC50: 63 (nM) from 1 assay(s)
	BindingDB:  5G3J	IC50: min: 1.2, max: 63 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.263	α = 90
b = 84.263	β = 90
c = 106.678	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Berger, M., Edman, K., Wissler, L., Neuhaus, R., Rehwinkel, H., Schacke, H., Jaroch, S.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection
• Version 1.2: 2019-04-03
  Changes: Data collection, Source and taxonomy