3M9F

HIV protease complexed with compound 10b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Epsilon substituted lysinol derivatives as HIV-1 protease inhibitors.

Jones, K.L.Holloway, M.K.Su, H.P.Carroll, S.S.Burlein, C.Touch, S.DiStefano, D.J.Sanchez, R.I.Williams, T.M.Vacca, J.P.Coburn, C.A.

(2010) Bioorg Med Chem Lett 20: 4065-4068

  • DOI: 10.1016/j.bmcl.2010.05.082
  • Primary Citation of Related Structures:  
    3M9F

  • PubMed Abstract: 
  • A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors ...

    A series of HIV-1 protease inhibitors containing an epsilon substituted lysinol backbone was synthesized. Two novel synthetic routes using N-boc-L-glutamic acid alpha-benzyl ester and 2,6-diaminopimelic acid were developed. Incorporation of this epsilon substituent enabled access to the S2 pocket of the enzyme, affording high potency inhibitors. Modeling studies and synthetic efforts suggest the potency increase is due to both conformational bias and van der Waals interactions with the S2 pocket.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. kristen_jones@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 proteaseAB99Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for Q9WFL7 (Human immunodeficiency virus 1)
Explore Q9WFL7 
Go to UniProtKB:  Q9WFL7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
595
Query on 595

Download CCD File 
A, B
N-[(1S,5S)-5-{[(4-aminophenyl)sulfonyl](3-methylbutyl)amino}-1-methyl-6-oxohexyl]-Nalpha-(methoxycarbonyl)-beta-phenyl-L-phenylalaninamide
C35 H46 N4 O6 S
JSZGHYRPBNJGPM-ZMAXYJRFSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
595IC50 :  0.007000000216066837   nM  PDBBind
595IC50:  0.007000000216066837   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.173α = 90
b = 85.934β = 90
c = 46.134γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-03-22 
  • Released Date: 2010-06-30 
  • Deposition Author(s): Su, H.P.

Revision History 

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description