5SZ9

Structure-based design of a new series of N-piperidin-3-ylpyrimidine-5-carboxamides as renin inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of a new series of N-(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors.

Imaeda, Y.Tawada, M.Suzuki, S.Tomimoto, M.Kondo, M.Tarui, N.Sanada, T.Kanagawa, R.Snell, G.Behnke, C.A.Kubo, K.Kuroita, T.

(2016) Bioorg.Med.Chem. 24: 5771-5780

  • DOI: 10.1016/j.bmc.2016.09.030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The action of the aspartyl protease renin is the rate-limiting initial step of the renin-angiotensin-aldosterone system. Therefore, renin is a particularly promising target for blood pressure as well as onset and progression of cardiovascular and ren ...

    The action of the aspartyl protease renin is the rate-limiting initial step of the renin-angiotensin-aldosterone system. Therefore, renin is a particularly promising target for blood pressure as well as onset and progression of cardiovascular and renal diseases. New pyrimidine derivatives 5-14 were designed in an attempt to enhance the renin inhibitory activity of compound 3 identified by our previous fragment-based drug design approach. Introduction of a basic amine essential for interaction with the two aspartic acids in the catalytic site and optimization of the S1/S3 binding elements including an induced-fit structural change of Leu114 ('Leu-in' to 'Leu-out') by a rational structure-based drug design approach led to the discovery of N-(piperidin-3-yl)pyrimidine-5-carboxamide 14, a 65,000-fold more potent renin inhibitor than compound 3. Surprisingly, this remarkable enhancement in the inhibitory activity of compound 14 has been achieved by the overall addition of only seven heavy atoms to compound 3. Compound 14 demonstrated excellent selectivity over other aspartyl proteases and moderate oral bioavailability in rats.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraoka-Higashi, 2-Chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: yasuhiro.imaeda@takeda.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Renin
A, B
339Homo sapiensMutation(s): 0 
Gene Names: REN
EC: 3.4.23.15
Find proteins for P00797 (Homo sapiens)
Go to Gene View: REN
Go to UniProtKB:  P00797
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
74Y
Query on 74Y

Download SDF File 
Download CCD File 
A, B
(azepan-1-yl)(2-{[(furan-2-yl)methyl]amino}-6-methylpyridin-3-yl)methanone
C18 H23 N3 O2
JCTPWJNVLSRFOU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.184 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 140.129α = 90.00
b = 140.129β = 90.00
c = 140.129γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references