4RYG | pdb_00004ryg

RENIN IN COMPLEXED WITH N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrrolidin-3-yl}methyl)-4-methoxy-3-(3-methoxypropoxy)-N-(propan-2-yl)benzamide INHIBITOR

PDB DOI: https://doi.org/10.2210/pdb4RYG/pdb

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

Deposited: 2014-12-15 Released: 2015-03-25
Deposition Author(s): Ostermann, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.183 (Depositor), 0.188 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

trans-(3S,4S)-Disubstituted pyrrolidines as inhibitors of the human aspartyl protease renin. Part I: Prime site exploration using an amino linker.

Lorthiois, E., Cumin, F., Ehrhardt, C., Kosaka, T., Sellner, H., Ostermann, N., Francotte, E., Wagner, T., Maibaum, J.

(2015) Bioorg Med Chem Lett 25: 1782-1786

PubMed: 25782742 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2015.02.039
Primary Citation Related Structures:
4RYC, 4RYG

PubMed Abstract:
Recently, we reported on the discovery of (3S,4S)-disubstituted pyrrolidines (e.g., 2) as inhibitors of the human aspartyl protease renin. In our effort to further expand the scope of this novel class of direct renin inhibitors, a new sub-series was designed in which the prime site substituents are linked to the pyrrolidine core by a (3S)-amino functional group. In particular, analogs bearing the corresponding sulfonamide spacer (50, 51 and 54a) demonstrated a pronounced increase in in vitro potency compared to compound 2.

Organizational Affiliation

Novartis Pharma AG, Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland. Electronic address: edwige.lorthiois@novartis.com.

Macromolecule Content

Total Structure Weight: 76.3 kDa
Atom Count: 5,442
Modeled Residue Count: 673
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	340	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00797
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P00797-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3ZJ Query on 3ZJ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	N-({(3S,4S)-4-[(benzylsulfonyl)amino]pyrrolidin-3-yl}methyl)-4-methoxy-3-(3-methoxypropoxy)-N-(propan-2-yl)benzamide C₂₇ H₃₉ N₃ O₆ S WPSURGXSNWIBBJ-BJKOFHAPSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	H [auth B], I [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
3ZJ	BindingDB: 4RYG	IC50: min: 3, max: 8 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.183 (Depositor), 0.188 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.674	α = 90
b = 141.674	β = 90
c = 141.674	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Ostermann, N.

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2015-04-08
Changes: Database references
Version 1.2: 2015-04-22
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2021-06-30
Changes: Data collection, Structure summary
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Structure summary