3OQK

Crystal Structure Analysis of Renin-indole-piperazin inhibitor complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery and optimization of a new class of potent and non-chiral indole-3-carboxamide-based renin inhibitors.

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

(2010) Bioorg Med Chem Lett 20: 6268-6272

  • DOI: 10.1016/j.bmcl.2010.08.092
  • Primary Citation of Related Structures:  
    3OOT, 3OQF, 3OQK

  • PubMed Abstract: 
  • Selective inhibition of the aspartyl protease renin has gained attraction as an interesting approach to control hypertension and associated cardiovascular risk factors given its unique position in the renin-angiotensin system. Using a combination of high-throughput screening, parallel synthesis, X-ray crystallography and structure-based design, we identified and optimized a novel series of potent and non-chiral indole-3-carboxamides with remarkable potency for renin ...

    Selective inhibition of the aspartyl protease renin has gained attraction as an interesting approach to control hypertension and associated cardiovascular risk factors given its unique position in the renin-angiotensin system. Using a combination of high-throughput screening, parallel synthesis, X-ray crystallography and structure-based design, we identified and optimized a novel series of potent and non-chiral indole-3-carboxamides with remarkable potency for renin. The most potent compound 5k displays an IC(50) value of 2nM.


    Organizational Affiliation

    Sanofi-Aventis Deutschland GmbH, Chemical and Analytical Sciences, Building G878, D-65926 Frankfurt, Germany. Bodo.Scheiper@sanofi-aventis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ReninA, B340Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00797
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S52
Query on S52

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
2-phenoxy-1-phenyl-3-(piperazin-1-ylcarbonyl)-1H-indole
C25 H23 N3 O2
PAQQZWUEZAUGRI-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
S52 PDBBind:  3OQK IC50: 420 (nM) from 1 assay(s)
BindingDB:  3OQK IC50: 420 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.387α = 90
b = 141.387β = 90
c = 141.387γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2010-09-03 
  • Released Date: 2010-10-27 
  • Deposition Author(s): Bocskei, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary