5L7H

MCR IN COMPLEX WITH ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Drug Design of Mineralocorticoid Receptor Antagonists to Explore Oxosteroid Receptor Selectivity.

Nordqvist, A.O'Mahony, G.Friden-Saxin, M.Fredenwall, M.Hogner, A.Granberg, K.L.Aagaard, A.Backstrom, S.Gunnarsson, A.Kaminski, T.Xue, Y.Dellsen, A.Hansson, E.Hansson, P.Ivarsson, I.Karlsson, U.Bamberg, K.Hermansson, M.Georgsson, J.Lindmark, B.Edman, K.

(2017) ChemMedChem 12: 50-65

  • DOI: 10.1002/cmdc.201600529
  • Primary Citation of Related Structures:  
    5L7H, 5L7E, 5L7G

  • PubMed Abstract: 
  • The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in the regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of nonsteroidal MR antagonists to improve selectivity over ...

    The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in the regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of nonsteroidal MR antagonists to improve selectivity over other members of the oxosteroid receptor family. A biaryl sulfonamide compound was identified in a high-throughput screening (HTS) campaign. The compound bound to MR with pK i =6.6, but displayed poor selectivity over the glucocorticoid receptor (GR) and the progesterone receptor (PR). Following X-ray crystallography of MR in complex with the HTS hit, a compound library was designed that explored an induced-fit hypothesis that required movement of the Met852 side chain. An improvement in MR selectivity of 11- to 79-fold over PR and 23- to 234-fold over GR was obtained. Given the U-shaped binding conformation, macrocyclizations were explored, yielding a macrocycle that bound to MR with pK i =7.3. Two protein-ligand X-ray structures were determined, confirming the hypothesized binding mode for the designed compounds.


    Organizational Affiliation

    Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mineralocorticoid receptor A305Homo sapiensMutation(s): 0 
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 B10Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6QG
Query on 6QG

Download Ideal Coordinates CCD File 
A
3-methyl-5,8-dioxa-17lambda-thia-4,18-diazatetracyclo[18.2.2.1,.0]pentacosa-1(22),2(6),3,9,11,13(25),20,23-octaene-17,17-dione
C21 H22 N2 O4 S
XUNBRRXZHVGCEW-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download Ideal Coordinates CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6QGKi:  50   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.67α = 90
b = 77.89β = 90
c = 78.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Source and taxonomy
  • Version 1.3: 2019-10-16
    Changes: Data collection