2QNN

HIV-1 protease in complex with a multiple decorated pyrrolidine-based inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure-Guided Design of C2-Symmetric HIV-1 Protease Inhibitors Based on a Pyrrolidine Scaffold.

Blum, A., Bottcher, J., Heine, A., Klebe, G., Diederich, W.E.

(2008) J.Med.Chem. 51: 2078-2087

  • DOI: 10.1021/jm701142s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Infections with the human immunodeficiency virus, which inevitably lead to the development of AIDS, are still among the most serious global health problems causing more than 2.5 million deaths per year. In the pathophysiological processes of this pan ...

    Infections with the human immunodeficiency virus, which inevitably lead to the development of AIDS, are still among the most serious global health problems causing more than 2.5 million deaths per year. In the pathophysiological processes of this pandemic, HIV protease has proven to be an invaluable drug target because of its essential role in the virus' replication process. By use of pyrrolidine as core structure, symmetric 3,4-bis-N-alkylsulfonamides were designed and synthesized enantioselectively from D-(-)-tartaric acid as a new class of HIV protease inhibitors. Structure-guided design using the cocrystal structure of an initial lead as starting point resulted in a second series of inhibitors with improved affinity. The binding modes of four representatives were determined by X-ray crystallography to elucidate the underlying factors accounting for the SAR. With this information for further rational design, the combination of suitable side chains resulted in a final inhibitor showing a significantly improved affinity of K(i) = 74 nM.

    Organizational Affiliation: 

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein (Pr160Gag-Pol)
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
QN1
Query on QN1
Download SDF File 
Download CCD File 
B
4,4'-[(3S,4S)-pyrrolidine-3,4-diylbis({[4-(trifluoromethyl)benzyl]imino}sulfonyl)]dibenzamide
C34 H31 F6 N5 O6 S2
QVMBQAVVCRRZFT-KYJUHHDHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QN1Ki: 70 nM BINDINGMOAD
QN1Ki: 70 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.384α = 90.00
b = 86.179β = 90.00
c = 46.290γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MAR345dtbdata collection
SHELXmodel building
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance