3WFG | pdb_00003wfg

Mineralocorticoid receptor ligand-binding domain with compuond 2e


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.179 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design, synthesis, and structure-activity relationships of dihydrofuran-2-one and dihydropyrrol-2-one derivatives as novel benzoxazin-3-one-based mineralocorticoid receptor antagonists.

Hasui, T.Ohra, T.Ohyabu, N.Asano, K.Matsui, H.Mizukami, A.Habuka, N.Sogabe, S.Endo, S.Siedem, C.S.Tang, T.P.Gauthier, C.De Meese, L.A.Boyd, S.A.Fukumoto, S.

(2013) Bioorg Med Chem 21: 5983-5994

  • DOI: https://doi.org/10.1016/j.bmc.2013.07.043
  • Primary Citation Related Structures: 
    3WFF, 3WFG

  • PubMed Abstract: 

    Dihydrofuran-2-one and dihydropyrrol-2-one derivatives were identified as novel, potent and selective mineralocorticoid receptor (MR) antagonists by the structure-based drug design approach utilizing the crystal structure of MR/compound complex. Introduction of lipophilic substituents directed toward the unfilled spaces of the MR and identification of a new scaffold, dihydropyrrol-2-one ring, led to potent in vitro activity. Among the synthesized compounds, dihydropyrrol-2-one 11i showed an excellent in vitro activity (MR binding IC50=43nM) and high selectivity over closely related steroid receptors such as the androgen receptor (AR), progesterone receptor (PR) and glucocorticoid receptor (GR) (>200-fold for AR and PR, 100-fold for GR).


  • Organizational Affiliation
    • Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-higashi, 2-Chome, Fujisawa, Kanagawa 251-8555, Japan. tomoaki.hasui@takeda.com

Macromolecule Content 

  • Total Structure Weight: 32.81 kDa 
  • Atom Count: 2,366 
  • Modeled Residue Count: 249 
  • Deposited Residue Count: 275 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mineralocorticoid receptor275Homo sapiensMutation(s): 3 
Gene Names: NR3C2MCRMLR
UniProt & NIH Common Fund Data Resources
Find proteins for P08235 (Homo sapiens)
Explore P08235 
Go to UniProtKB:  P08235
PHAROS:  P08235
GTEx:  ENSG00000151623 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08235
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WFG

Query on WFG



Download:Ideal Coordinates CCD File
B [auth A]6-[(2S)-4-(4-fluorophenyl)-2-methyl-5-oxo-2,5-dihydrofuran-3-yl]-2H-1,4-benzoxazin-3(4H)-one
C19 H14 F N O4
FLUKKJOWQPEDIT-JTQLQIEISA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.179 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.403α = 90
b = 66.813β = 90
c = 75.252γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description