1K6V

LACK OF SYNERGY FOR INHIBITORS TARGETING A MULTI-DRUG RESISTANT HIV-1 PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease.

King, N.M.Melnick, L.Prabu-Jeyabalan, M.Nalivaika, E.A.Yang, S.S.Gao, Y.Nie, X.Zepp, C.Heefner, D.L.Schiffer, C.A.

(2002) Protein Sci. 11: 418-429

  • DOI: 10.1110/ps.25502
  • Primary Citation of Related Structures:  1K6C, 1K6P, 1K6T

  • PubMed Abstract: 
  • The three-dimensional structures of indinavir and three newly synthesized indinavir analogs in complex with a multi-drug-resistant variant (L63P, V82T, I84V) of HIV-1 protease were determined to approximately 2.2 A resolution. Two of the three analog ...

    The three-dimensional structures of indinavir and three newly synthesized indinavir analogs in complex with a multi-drug-resistant variant (L63P, V82T, I84V) of HIV-1 protease were determined to approximately 2.2 A resolution. Two of the three analogs have only a single modification of indinavir, and their binding affinities to the variant HIV-1 protease are enhanced over that of indinavir. However, when both modifications were combined into a single compound, the binding affinity to the protease variant was reduced. On close examination, the structural rearrangements in the protease that occur in the tightest binding inhibitor complex are mutually exclusive with the structural rearrangements seen in the second tightest inhibitor complex. This occurs as adaptations in the S1 pocket of one monomer propagate through the dimer and affect the conformation of the S1 loop near P81 of the other monomer. Therefore, structural rearrangements that occur within the protease when it binds to an inhibitor with a single modification must be accounted for in the design of inhibitors with multiple modifications. This consideration is necessary to develop inhibitors that bind sufficiently tightly to drug-resistant variants of HIV-1 protease to potentially become the next generation of therapeutic agents.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL polyprotein
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P35963 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P35963
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
XN2
Query on XN2

Download SDF File 
Download CCD File 
B
N-[2-HYDROXY-1-INDANYL]-5-[(2-TERTIARYBUTYLAMINOCARBONYL)-4(BENZO[1,3]DIOXOL-5-YLMETHYL)-PIPERAZINO]-4-HYDROXY-2-(1-PHENYLETHYL)-PENTANAMIDE
ANALOGUE OF INDINAVIR DRUG
C39 H50 N4 O6
MJIRDPUZGGHJMX-OIVSQUILSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XN2Kd: 120 nM BINDINGMOAD
XN2Kd: 120 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.445α = 90.00
b = 59.404β = 90.00
c = 61.743γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-10-17 
  • Released Date: 2002-02-06 
  • Deposition Author(s): Schiffer, C.A.

Revision History 

  • Version 1.0: 2002-02-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance