3CCZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5HI
Query on 5HI

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], J [auth C], L [auth D](3R,5R)-7-[2-(4-fluorophenyl)-4-{[(1S)-2-hydroxy-1-phenylethyl]carbamoyl}-5-(1-methylethyl)-1H-imidazol-1-yl]-3,5-dihydroxyheptanoic acid
C28 H34 F N3 O6
YBLASZBVZVCRFU-DNVJHFABSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], I [auth C], K [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5HI-TΔS:  1.6699999570846558   kJ/mol  BindingDB
5HIKd :  51.70000076293945   nM  PDBBind
5HIΔG:  42.220001220703125   kJ/mol  BindingDB
5HIKd:  51.70000076293945   nM  Binding MOAD
5HIΔG:  41.380001068115234   kJ/mol  BindingDB
5HI-TΔS:  10.460000038146973   kJ/mol  BindingDB
5HI-TΔS:  18.799999237060547   kJ/mol  BindingDB
5HIΔG:  44.310001373291016   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.862α = 90
b = 135.655β = 97.16
c = 83.148γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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