3SFC

Structure-Based Optimization of Potent 4- and 6-Azaindole-3-Carboxamides as Renin Inhibitors

PDB DOI: https://doi.org/10.2210/pdb3SFC/pdb

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

Deposited: 2011-06-13 Released: 2011-08-31
Deposition Author(s): Scheiper, B., Matter, H., Steinhagen, H., Bocskei, Z., Fleury, V., McCort, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243
R-Value Work: 0.211
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-based optimization of potent 4- and 6-azaindole-3-carboxamides as renin inhibitors.

Scheiper, B., Matter, H., Steinhagen, H., Bocskei, Z., Fleury, V., McCort, G.

(2011) Bioorg Med Chem Lett 21: 5480-5486

PubMed: 21840218 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.06.114
Primary Citation of Related Structures:
3SFC

PubMed Abstract:
The control of hypertension and associated cardiovascular risk factors is possible by selective inhibition of the aspartyl protease renin due to its unique position in the renin-angiotensin system. Starting from a previously disclosed series of potent and nonchiral indole-3-carboxamides, we further explored this motif by structure-based drug design guided by X-ray crystallography in combination with efficient parallel synthesis. This resulted in the discovery of 4- or 6-azaindole derivatives with remarkable potency for renin inhibition. The best compound from these series showed an IC(50) value of 1.3 nM.

Organizational Affiliation

Sanofi-Aventis, Deutschland GmbH, Chemical and Analytical Sciences, Building G878, D-65926 Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 76.91 kDa
Atom Count: 5,894
Modelled Residue Count: 680
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Renin	A, B	340	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S53 Query on S53 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A]	G [auth A], H [auth A], K [auth B]	[7-benzyl-2-(5-fluoro-2-methylphenoxy)-1-phenyl-1H-pyrrolo[2,3-c]pyridin-3-yl](piperazin-1-yl)methanone C₃₂ H₂₉ F N₄ O₂ UIBPLELQTBSRIZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B]	C [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	D [auth A], E [auth A], F [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
S53	BindingDB: 3SFC	IC50: min: 3, max: 226 (nM) from 3 assay(s)
	Binding MOAD: 3SFC	IC50: 3 (nM) from 1 assay(s)
	PDBBind: 3SFC	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.243
R-Value Work: 0.211
R-Value Observed: 0.212
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.794	α = 90
b = 138.794	β = 90
c = 138.794	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
AMoRE	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2012-05-23
Changes: Database references
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary