6GGG

Mineralocorticoid receptor in complex with (s)-13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

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

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mineralocorticoid receptor A305Homo sapiensMutation(s): 3 
Gene Names: NR3C2MCRMLR
Find proteins for P08235 (Homo sapiens)
Explore P08235 
Go to UniProtKB:  P08235
NIH Common Fund Data Resources
PHAROS:  P08235
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NCOA1 peptide B15Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EYN
Query on EYN

Download Ideal Coordinates CCD File 
A
2-[(3~{S})-7-fluoranyl-6-(2-methylpropyl)-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]-~{N}-methyl-ethanamide
C24 H26 F N3 O5
OUCNRPREOGLYEL-INIZCTEOSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EYNKi:  0.6299999952316284   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.729α = 90
b = 75.729β = 90
c = 121.238γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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