3O9L

Design and optimisation of new piperidines as renin inhibitors

PDB DOI: https://doi.org/10.2210/pdb3O9L/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2010-08-04 Released: 2011-03-02
Deposition Author(s): Corminboeuf, O., Bezencon, O., Grisostomi, C., Remen, L., Richard-Bildstein, S., Bur, D., Prade, L., Hess, P., Strickner, P., Treiber, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.307
R-Value Work: 0.245
R-Value Observed: 0.248

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Design and optimization of new piperidines as renin inhibitors.

Corminboeuf, O., Bezencon, O., Grisostomi, C., Remen, L., Richard-Bildstein, S., Bur, D., Prade, L., Hess, P., Strickner, P., Fischli, W., Steiner, B., Treiber, A.

(2010) Bioorg Med Chem Lett 20: 6286-6290

PubMed: 20843686 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.08.086
Primary Citation of Related Structures:
3O9L, 3OAD, 3OAG

PubMed Abstract:
The discovery of a new series of piperidine-based renin inhibitors is described herein. SAR optimization upon the P3 renin sub-pocket is described, leading to the discovery of 9 and 41, two bioavailable renin inhibitors orally active at low doses in a transgenic rat model of hypertension.

Organizational Affiliation

Drug Discovery Chemistry & Biochemistry, Actelion Pharmaceuticals Ltd, Gewerbestrasse 16, 4123 Allschwil, Switzerland.

Macromolecule Content

Total Structure Weight: 76.85 kDa
Atom Count: 5,352
Modelled Residue Count: 670
Deposited Residue Count: 684
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, C	166	Homo sapiens	Mutation(s): 0 Gene Names: REN EC: 3.4.23.15
UniProt & NIH Common Fund Data Resources
Find proteins for P00797 (Homo sapiens) Explore P00797 Go to UniProtKB: P00797
PHAROS: P00797 GTEx: ENSG00000143839
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00797
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P00797-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	B, D	176	Homo sapiens	Mutation(s): 0 Gene Names: REN EC: 3.4.23.15
UniProt & NIH Common Fund Data Resources
Find proteins for P00797 (Homo sapiens) Explore P00797 Go to UniProtKB: P00797
PHAROS: P00797 GTEx: ENSG00000143839
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00797
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LPN Query on LPN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth C]	F [auth A], G [auth C]	(3R,4S)-N-[2-chloro-5-(3-methoxypropyl)benzyl]-N-cyclopropyl-4-{4-[2-(2,6-dichloro-4-methylphenoxy)ethoxy]phenyl}piperidine-3-carboxamide C₃₅ H₄₁ Cl₃ N₂ O₄ RDCUZWVELSAOBC-IHLOFXLRSA-N		Interactions Focus chain F [auth A] Focus chain G [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
LPN	PDBBind: 3O9L	IC50: 0.22 (nM) from 1 assay(s)
LPN	BindingDB: 3O9L	IC50: min: 0.22, max: 11.8 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.307
R-Value Work: 0.245
R-Value Observed: 0.248
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.031	α = 90
b = 90.366	β = 90
c = 120.774	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-02

Deposition Author(s):

Richard-Bildstein, S.

Revision History (Full details and data files)

Version 1.0: 2011-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Structure summary