Biological Assembly 1  

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

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: 37.07 kDa 
• Atom Count: 2341 
• Modelled Residue Count: 252 
• Deposited Residue Count: 320 
• Unique protein chains: 2

6GG8

Mineralocorticoid receptor in complex with (s)-13

• PDB DOI: 10.2210/pdb6GG8/pdb

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


• Deposited: 2018-05-03 Released: 2019-01-09 
• Deposition Author(s): Edman, K., Aagaard, A., Tangefjord, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Literature

Identification of Mineralocorticoid Receptor Modulators with Low Impact on Electrolyte Homeostasis but Maintained Organ Protection.

Granberg, K.L., Yuan, Z.Q., Lindmark, B., Edman, K., Kajanus, J., Hogner, A., Malmgren, M., O'Mahony, G., Nordqvist, A., Lindberg, J., Tangefjord, S., Kossenjans, M., Lofberg, C., Branalt, J., Liu, D., Selmi, N., Nikitidis, G., Nordberg, P., Hayen, A., Aagaard, A., Hansson, E., Hermansson, M., Ivarsson, I., Jansson-Lofmark, R., Karlsson, U., Johansson, U., William-Olsson, L., Hartleib-Geschwindner, J., Bamberg, K.

(2019) J Med Chem 62: 1385-1406

• PubMed: 30596500 
• DOI: 10.1021/acs.jmedchem.8b01523
• Primary Citation of Related Structures:  
  6GEV, 6GG8, 6GGG


• PubMed Abstract: 
  

The mechanism-based risk for hyperkalemia has limited the use of mineralocorticoid receptor antagonists (MRAs) like eplerenone in cardio-renal diseases. Here, we describe the structure and property-driven lead generation and optimization, which resulted in identification of MR modulators ( S)-1 and ( S)-33. Both compounds were partial MRAs but still demonstrated equally efficacious organ protection as eplerenone after 4 weeks of treatment in uni-nephrectomized rats on high-salt diet and aldosterone infusion. Importantly, and in sharp contrast to eplerenone, this was achieved without substantial changes to the urine Na ⁺ /K ⁺ ratio after acute treatment in rat, which predicts a reduced risk for hyperkalemia. This work led to selection of ( S)-1 (AZD9977) as the clinical candidate for treating MR-mediated cardio-renal diseases, including chronic kidney disease and heart failure. On the basis of our findings, we propose an empirical model for prediction of compounds with low risk of affecting the urinary Na ⁺ /K ⁺ ratio in vivo.

---

Organizational Affiliation: 

Pharmaron Beijing Co., Ltd. , No. 6 Taihe Road, BDA , Beijing 100176 , P. R. China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mineralocorticoid receptor	A	305	Homo sapiens	Mutation(s): 0  Gene Names: NR3C2, MCR, MLR
UniProt & NIH Common Fund Data Resources
Find proteins for P08235 (Homo sapiens) Explore P08235  Go to UniProtKB:  P08235
PHAROS:  P08235 GTEx:  ENSG00000151623

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0  Gene Names: NCOA1, BHLHE74, SRC1 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EY8	D [auth A]	[(3~{R})-7-fluoranyl-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]methanesulfonamide C18 H16 F N3 O6 S FDWPXNLUFQNWMH-GFCCVEGCSA-N
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EY8	Binding MOAD:  6GG8	Ki: 0.79 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.654	α = 90
b = 77.953	β = 90
c = 78.755	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-05-03 
• Released Date: 2019-01-09 
Deposition Author(s): Edman, K., Aagaard, A., Tangefjord, S.

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Database references