4Q1N

Structure-based design of 4-hydroxy-3,5-substituted piperidines as direct renin inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-based design of substituted piperidines as a new class of highly efficacious oral direct Renin inhibitors.

Ehara, T.Irie, O.Kosaka, T.Kanazawa, T.Breitenstein, W.Grosche, P.Ostermann, N.Suzuki, M.Kawakami, S.Konishi, K.Hitomi, Y.Toyao, A.Gunji, H.Cumin, F.Schiering, N.Wagner, T.Rigel, D.F.Webb, R.L.Maibaum, J.Yokokawa, F.

(2014) ACS Med Chem Lett 5: 787-792

  • DOI: 10.1021/ml500137b
  • Primary Citation of Related Structures:  
    4Q1N, 4PYV

  • PubMed Abstract: 
  • A cis-configured 3,5-disubstituted piperidine direct renin inhibitor, (syn,rac)-1, was discovered as a high-throughput screening hit from a target-family tailored library. Optimization of both the prime and the nonprime site residues flanking the cen ...

    A cis-configured 3,5-disubstituted piperidine direct renin inhibitor, (syn,rac)-1, was discovered as a high-throughput screening hit from a target-family tailored library. Optimization of both the prime and the nonprime site residues flanking the central piperidine transition-state surrogate resulted in analogues with improved potency and pharmacokinetic (PK) properties, culminating in the identification of the 4-hydroxy-3,5-substituted piperidine 31. This compound showed high in vitro potency toward human renin with excellent off-target selectivity, 60% oral bioavailability in rat, and dose-dependent blood pressure lowering effects in the double-transgenic rat model.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research , Ohkubo 8, Tsukuba, Ibaraki 300-2611, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ReninA, B340Homo sapiensMutation(s): 0 
Gene Names: REN
EC: 3.4.23.15
Find proteins for P00797 (Homo sapiens)
Explore P00797 
Go to UniProtKB:  P00797
NIH Common Fund Data Resources
PHAROS  P00797
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2Y9
Query on 2Y9

Download CCD File 
A, B
(3S,4R,5R)-N-cyclopropyl-N'-[(2R)-1-ethoxy-4-methylpentan-2-yl]-4-hydroxy-N-[5-(propan-2-yl)pyridin-2-yl]piperidine-3,5-dicarboxamide
C26 H42 N4 O4
YOVGCKBDPOHLAV-CNIHBODFSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2Y9IC50:  0.20000000298023224   nM  BindingDB
2Y9IC50:  2   nM  BindingDB
2Y9IC50:  0.6000000238418579   nM  BindingDB
2Y9IC50:  0.20000000298023224   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.854α = 90
b = 140.854β = 90
c = 140.854γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary