1C6X

ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease.

Munshi, S.Chen, Z.Yan, Y.Li, Y.Olsen, D.B.Schock, H.B.Galvin, B.B.Dorsey, B.Kuo, L.C.

(2000) Acta Crystallogr.,Sect.D 56: 381-388

  • Primary Citation of Related Structures:  1C6Y, 1C6Z, 1C70

  • PubMed Abstract: 
  • Structures of the complexes of HIV protease inhibitor L--756,423 with the HIV-1 wild-type protease and of the inhibitors Indinavir, L-739,622 and Saquinavir with the mutant protease (9X) containing nine point mutations (Leu10Val, Lys20Met, Leu24Ile, ...

    Structures of the complexes of HIV protease inhibitor L--756,423 with the HIV-1 wild-type protease and of the inhibitors Indinavir, L-739,622 and Saquinavir with the mutant protease (9X) containing nine point mutations (Leu10Val, Lys20Met, Leu24Ile, Ser37Asp, Met46Ile, Ile54Val, Leu63Pro, Ala71Val, Val82Thr) have been determined. Comparative analysis of these structures reveals an alternate binding pocket for the P1-P3 group of Indinavir and L--756, 423. The alternate binding pocket is a result of concerted structural change in the 80s loop (residues 79-82) of the protease. The 80s loop is pulled away from the active site in order to accommodate the P1-P3 group, which is sandwiched between the flap and the 80s loop. This structural change is observed for the complexes of the wild type as well as the 9X mutant protease. The study reveals that the 80s loop is an intrinsically flexible loop in the wild-type HIV-1 protease and that mutations in this loop are not necessary to result in conformational changes. Conformation of this loop in the complex depends primarily upon the nature of the bound inhibitor and may be influenced by mutations in the protease. The results underscore the need to understand the intrinsic structural plasticity of the protease for the design of effective inhibitors against the wild-type and drug-resistant enzyme forms. In addition, the alternate binding pocket for the P1-P3 group of Indinavir and L--756,423 may be exploited for the design of potent inhibitors.


    Related Citations: 
    • Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases
      Chen, Z.,Li, Y.,Chen, E.,Hall, D.L.,Darke, P.L.,Culberson, C.,Shafer, J.A.,Kuo, L.C.
      (1994) J.Biol.Chem. 269: 26344


    Organizational Affiliation

    Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA. sanjeev_munshi@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PROTEASE)
A, B
99Human immunodeficiency virus 1Gene Names: pol
Find proteins for O09893 (Human immunodeficiency virus 1)
Go to UniProtKB:  O09893
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3IN
Query on 3IN

Download SDF File 
Download CCD File 
B
N-[2(S)-CYCLOPENTYL-1(R)-HYDROXY-3(R)METHYL]-5-[(2(S)-TERTIARY-BUTYLAMINO-CARBONYL)-4-(N1-(2)-(N-METHYLPIPERAZINYL)-3-CHLORO-PYRAZINYL-5-CARBONYL)-PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYL-PENTANAMIDE
C37 H55 Cl N8 O5
SQZXWXXIPWXBCL-CYTJBAGBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.210α = 90.00
b = 88.210β = 90.00
c = 32.920γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-12-28 
  • Released Date: 2000-12-28 
  • Deposition Author(s): Munshi, S.

Revision History 

  • Version 1.0: 2000-12-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance