2IKU

Crystal Structure of Human Renin Complexed with Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.ab.2006.10.017
  • Primary Citation of Related Structures:  
    2IKO, 2IKU, 2IL2

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Renin
A, B
340Homo sapiensMutation(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
GTEx:  ENSG00000143839 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00797
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LIY
Query on LIY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
LIY PDBBind:  2IKU Kd: 79 (nM) from 1 assay(s)
BindingDB:  2IKU IC50: 58 (nM) from 1 assay(s)
-TΔS: 0.96 (kJ/mol) from 1 assay(s)
ΔG: -4.08e+1 (kJ/mol) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.162α = 90
b = 141.162β = 90
c = 141.162γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description