HIV-1 Protease in complex with a pyrrolidine-based inhibitor

Experimental Data Snapshot

  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jm701142s
  • Primary Citation of Related Structures:  
    2PQZ, 2PWC, 2PWR, 2QNN, 2QNP, 2QNQ

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
EC: (PDB Primary Data), (UniProt), (UniProt), (UniProt), (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Explore P03367 
Go to UniProtKB:  P03367
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03367
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
G0G Binding MOAD:  2PQZ Ki: 2150 (nM) from 1 assay(s)
PDBBind:  2PQZ Ki: 2150 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.53α = 90
b = 86β = 90
c = 46.72γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description