3OOT

Crystal Structure Analysis of Renin-indole-piperazin inhibitor complexes

• PDB DOI: https://doi.org/10.2210/pdb3OOT/pdb

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


• Deposited: 2010-08-31 Released: 2010-10-27 
• Deposition Author(s): Bocskei, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.220 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

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

• PubMed: 20850300 
• DOI: https://doi.org/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. The most potent compound 5k displays an IC(50) value of 2nM.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.89 kDa 
• Atom Count: 5,412 
• Modelled Residue Count: 674 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00797-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SSR	D [auth A], F [auth B]	2-(3-fluoro-2-methylbenzyl)-4-methyl-1-phenyl-3-(piperazin-1-ylcarbonyl)-1H-indol-5-ol C28 H28 F N3 O2 LWFGTVRNQYOUHL-UHFFFAOYSA-N
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SSR	BindingDB:  3OOT	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.220 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.554	α = 90
b = 143.554	β = 90
c = 143.554	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary