3M9F

HIV protease complexed with compound 10b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 

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

  • 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 epsi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for Q9WFL7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q9WFL7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
595
Query on 595

Download SDF File 
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 SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
595IC50: 0.007 nM BINDINGMOAD
595IC50: 0.007 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.173α = 90.00
b = 85.934β = 90.00
c = 46.134γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description