6GG8

Mineralocorticoid receptor in complex with (s)-13

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 

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): 0 
Gene Names: NR3C2, MCR, MLR
Find proteins for P08235 (Homo sapiens)
Explore P08235 
Go to UniProtKB:  P08235
NIH Common Fund Data Resources
PHAROS:  P08235
GTEx:  ENSG00000151623
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1 B15Homo sapiensMutation(s): 0 
Gene Names: NCOA1, BHLHE74, SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
GTEx:  ENSG00000084676
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EY8
Query on EY8
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EY8Ki:  0.7900000214576721   nM  Binding MOAD
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 = 48.654α = 90
b = 77.953β = 90
c = 78.755γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

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