3CD0

Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Thermodynamic and structure guided design of statin based inhibitors of 3-hydroxy-3-methylglutaryl coenzyme a reductase.

Sarver, R.W., Bills, E., Bolton, G., Bratton, L.D., Caspers, N.L., Dunbar, J.B., Harris, M.S., Hutchings, R.H., Kennedy, R.M., Larsen, S.D., Pavlovsky, A., Pfefferkorn, J.A., Bainbridge, G.

(2008) J Med Chem 51: 3804-3813

  • DOI: 10.1021/jm7015057
  • Primary Citation of Related Structures:  
    3CD0, 3CDA, 3CDB, 3CCT, 3CD5, 3CD7, 3CCW, 3CCZ

  • PubMed Abstract: 

    • Clinical studies have demonstrated that statins, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) inhibitors, are effective at lowering mortality levels associated with cardiovascular disease; however, 2-7% of patients may experience statin-induced myalgia that limits compliance with a treatment regimen ...

    Clinical studies have demonstrated that statins, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) inhibitors, are effective at lowering mortality levels associated with cardiovascular disease; however, 2-7% of patients may experience statin-induced myalgia that limits compliance with a treatment regimen. High resolution crystal structures, thermodynamic binding parameters, and biochemical data were used to design statin inhibitors with improved HMGR affinity and therapeutic index relative to statin-induced myalgia. These studies facilitated the identification of imidazole 1 as a potent (IC 50 = 7.9 nM) inhibitor with excellent hepatoselectivity (>1000-fold) and good in vivo efficacy. The binding of 1 to HMGR was found to be enthalpically driven with a Delta H of -17.7 kcal/M. Additionally, a second novel series of bicyclic pyrrole-based inhibitors was identified that induced order in a protein flap of HMGR. Similar ordering was detected in a substrate complex, but has not been reported in previous statin inhibitor complexes with HMGR.

    Organizational Affiliation: 

    Pfizer Global Research & Development, Ann Arbor, Michigan 48105, USA. Ronald.w.sarver@pfizer.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-hydroxy-3-methylglutaryl-coenzyme A reductaseA, B, C, D441Homo sapiensMutation(s): 1 
Gene Names: HMGCR
EC: 1.1.1.34
Find proteins for P04035 (Homo sapiens)
Explore P04035 
Go to UniProtKB:  P04035
NIH Common Fund Data Resources
PHAROS:  P04035
GTEx:  ENSG00000113161
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6HI
Query on 6HI
Download Ideal Coordinates CCD File 
 E [auth B], F [auth B], G [auth C], H [auth D](3R,5R)-7-{2-[(4-fluorobenzyl)carbamoyl]-4-(4-fluorophenyl)-1-(1-methylethyl)-1H-imidazol-5-yl}-3,5-dihydroxyheptanoic acid
C27 H31 F2 N3 O5
KNKKPGAQSAHIHV-FGZHOGPDSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6HIKd:  26.899999618530273   nM  Binding MOAD
6HIKd :  26.899999618530273   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.681α = 90
b = 173.957β = 119.06
c = 76.399γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description