3VHV

Mineralocorticoid receptor ligand-binding domain with non-steroidal antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report



Literature

Identification of Benzoxazin-3-one Derivatives as Novel, Potent, and Selective Nonsteroidal Mineralocorticoid Receptor Antagonists

Hasui, T.Matsunaga, N.Ora, T.Ohyabu, N.Nishigaki, N.Imura, Y.Igata, Y.Matsui, H.Motoyaji, T.Tanaka, T.Habuka, N.Sogabe, S.Ono, M.Siedem, C.S.Tang, T.P.Gauthier, C.De Meese, L.A.Boyd, S.A.Fukumoto, S.

(2011) J Med Chem 54: 8616-8631

  • DOI: 10.1021/jm2011645
  • Primary Citation of Related Structures:  
    3VHU, 3VHV

  • PubMed Abstract: 
  • Mineralocorticoid receptor (MR) blockade has come into focus as a promising approach for the treatment of cardiovascular diseases such as hypertension and congestive heart failure. In order to identify a novel class of nonsteroidal MR antagonists that ex ...

    Mineralocorticoid receptor (MR) blockade has come into focus as a promising approach for the treatment of cardiovascular diseases such as hypertension and congestive heart failure. In order to identify a novel class of nonsteroidal MR antagonists that exhibit significant potency and good selectivity over other steroidal hormone receptors, we designed a novel series of benzoxazin-3-one derivatives and synthesized them from 6-(7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl)-2H-1,4-benzoxazin-3(4H)-one (1a), high-throughput screening (HTS) hit compound. Our design was based on a crystal structure of an MR/compound complex and a docking model. In the course of lead generation from 1a, a 1,2-diaryl framework was characterized as a key structure with high binding affinity. On the basis of scaffold hopping and optimization studies, benzoxazin-3-one derivatives possessing 1-phenyl-3-trifluoromethylpyrazol-5-yl moiety at the 6-position were identified as a novel series of potent and selective MR antagonists. Among these compounds, 6-[1-(4-fluoro-2-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-5-yl]-2H-1,4-benzoxazin-3(4H)-one (14n) showed highly potent activity and good selectivity and also exhibited a significant antihypertensive effect in deoxycorticosterone acetate-salt hypertensive rats. On the basis of these results, compound 14n was progressed for further pharmacological evaluation.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Tomoaki_Hasui@takeda.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mineralocorticoid receptor A260Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LD2
Query on LD2

Download Ideal Coordinates CCD File 
A
6-[(1E)-2-phenyl-N-(3-sulfanyl-4H-1,2,4-triazol-4-yl)ethanimidoyl]-2H-1,4-benzoxazin-3(4H)-one
C18 H15 N5 O2 S
VWKIYKOULJUXRZ-HYARGMPZSA-N
 Ligand Interaction
LD1
Query on LD1

Download Ideal Coordinates CCD File 
A
6-[(7S)-7-phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl]-2H-1,4-benzoxazin-3(4H)-one
C18 H13 N5 O2 S
PAZOXNQSXSODTC-KRWDZBQOSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LD1IC50:  510   nM  Binding MOAD
LD1IC50 :  510   nM  PDBBind
LD1IC50:  510   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.142 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.612α = 90
b = 62.612β = 90
c = 75.504γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-09-07 
  • Released Date: 2011-12-28 
  • Deposition Author(s): Sogabe, S., Habuka, N.

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release