1C70

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: 0.270 
  • R-Value Work: 0.160 

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

  • DOI: 10.1107/s0907444900000469
  • Primary Citation of Related Structures:  

  • 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.

    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 1Mutation(s): 0 
Gene Names: pol
Find proteins for O92103 (Human immunodeficiency virus 1)
Go to UniProtKB:  O92103
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L75
Query on L75
Download SDF File 
Download CCD File 
B
N-[2(R)-HYDROXY-1(S)-INDANYL]-2(R)-PHENYLMETHYL-4(S)-HYDROXY-5-[4-[2-BENZOFURANYLMETHYL]-2(S)-[TERT-BUTYLAMINOCARBONYL]-PIPERAZINYL]-PENTANEAMIDE
L-756,423
C39 H48 N4 O5
AOMZDQMIOCTPQP-QHQMVRJISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L75Ki: 0.05 nM BINDINGMOAD
L75Ki: 0.05 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.860α = 90.00
b = 87.120β = 90.00
c = 46.970γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1999-12-29 
  • 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