2IKU

Crystal Structure of Human Renin Complexed with Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Binding thermodynamics of substituted diaminopyrimidine renin inhibitors.

Sarver, R.W.Peevers, J.Cody, W.L.Ciske, F.L.Dyer, J.Emerson, S.D.Hagadorn, J.C.Holsworth, D.D.Jalaie, M.Kaufman, M.Mastronardi, M.McConnell, P.Powell, N.A.Quin, J.Van Huis, C.A.Zhang, E.Mochalkin, I.

(2007) Anal.Biochem. 360: 30-40

  • DOI: 10.1016/j.ab.2006.10.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Renin is an aspartyl protease involved in the production of angiotensin II, a potent vasoconstrictor. Renin inhibitors can prevent blood vessel constriction and therefore could be useful for the treatment of hypertension. High-throughput screening ef ...

    Renin is an aspartyl protease involved in the production of angiotensin II, a potent vasoconstrictor. Renin inhibitors can prevent blood vessel constriction and therefore could be useful for the treatment of hypertension. High-throughput screening efforts identified a small molecule renin inhibitor with a core substituted diaminopyrimidine ring. Parallel medicinal chemistry efforts based on this lead resulted in compound 1. A complex of 1 bound to renin was crystallized, and structural data were obtained by X-ray diffraction. The structure indicated that there were adjacent unoccupied binding pockets. Synthetic efforts were initiated to extend functionality into these pockets so as to improve affinity and adjust pharmacokinetic parameters. Thermodynamics data for inhibitor binding to renin were also collected using isothermal titration calorimetry. These data were used to help guide inhibitor optimization by suggesting molecular alterations to improve binding affinity from both thermodynamic and structural perspectives. The addition of a methoxypropyl group extending into the S3 subpocket improved inhibitor affinity and resulted in greater binding enthalpy. Initial additions to the pyrimidine ring template that extended into the large hydrophobic S2 pocket did not improve affinity and dramatically altered the thermodynamic driving force for the binding interaction. Binding of the core template was enthalpically driven, whereas binding of initial inhibitors with S2 extensions was both enthalpically and entropically driven but lost significant binding enthalpy. Additional electrostatic interactions were then incorporated into the S2 extension to improve binding enthalpy while taking advantage of the favorable entropy.


    Organizational Affiliation

    Pfizer Global Research and Development, Ann Arbor, MI 48105, USA. ronald.w.sarver@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Renin
A, B
340Homo sapiensMutation(s): 0 
Gene Names: REN
EC: 3.4.23.15
Find proteins for P00797 (Homo sapiens)
Go to Gene View: REN
Go to UniProtKB:  P00797
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIY
Query on LIY

Download SDF File 
Download CCD File 
A, B
6-ETHYL-5-[(2S)-1-(3-METHOXYPROPYL)-2-PHENYL-1,2,3,4-TETRAHYDROQUINOLIN-7-YL]PYRIMIDINE-2,4-DIAMINE
C25 H31 N5 O
UOYVKYJWAXJTTE-NRFANRHFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LIYΔG: -40.8 kJ/mol (100) BINDINGDB
LIYIC50: 58 nM (100) BINDINGDB
LIYKd: 79 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 141.162α = 90.00
b = 141.162β = 90.00
c = 141.162γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-10-02 
  • Released Date: 2006-12-05 
  • Deposition Author(s): Mochalkin, I.

Revision History 

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description