1BV7

COUNTERACTING HIV-1 PROTEASE DRUG RESISTANCE: STRUCTURAL ANALYSIS OF MUTANT PROTEASES COMPLEXED WITH XV638 AND SD146, CYCLIC UREA AMIDES WITH BROAD SPECIFICITIES

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities.

Ala, P.J., Huston, E.E., Klabe, R.M., Jadhav, P.K., Lam, P.Y., Chang, C.H.

(1998) Biochemistry 37: 15042-15049

  • DOI: 10.1021/bi980386e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The long-term therapeutic benefit of HIV antiretroviral therapy is still threatened by drug-resistant variants. Mutations in the S1 subsite of the protease are the primary cause for the loss of sensitivity toward many HIV protease inhibitors, includi ...

    The long-term therapeutic benefit of HIV antiretroviral therapy is still threatened by drug-resistant variants. Mutations in the S1 subsite of the protease are the primary cause for the loss of sensitivity toward many HIV protease inhibitors, including our first-generation cyclic urea-based inhibitors DMP323 and DMP450. We now report the structures of the three active-site mutant proteases V82F, I84V, and V82F/I84V in complex with XV638 and SD146, two P2 analogues of DMP323 that are 8-fold more potent against the wild type and are able to inhibit a broad panel of drug-resistant variants [Jadhav, P. K., et al. (1997) J. Med. Chem. 40, 181-191]. The increased efficacy of XV638 and SD146 is due primarily to an increase in P2-S2 interactions: 30-40% more van der Waals contacts and two to four additional hydrogen bonds. Furthermore, because these new interactions do not perturb other subsites in the protease, it appears that the large complementary surface areas of their P2 substituents compensate for the loss of P1-S1 interactions and reduce the probability of selecting for drug-resistant variants.

    Organizational Affiliation: 

    Experimental Station, DuPont Pharmaceuticals, Wilmington, Delaware 19880, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HIV-1 PROTEASE)
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XV6
Query on XV6
Download SDF File 
Download CCD File 
A
[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-3,3'-[[TETRAHYDRO-5,6-DIHYDROXY-2-OXO-4,7-BIS(PHENYLMETHYL)-1H-1,3-DIAZEPINE-1,3(2H)-DIYL] BIS(METHYLENE)]BIS[N-2-THIAZOLYLBENZAMIDE]
XV638
C41 H38 N6 O5 S2
JDALSSGOBMTZEP-NWJWHWDBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XV6Ki: 0.5 nM BINDINGMOAD
XV6Ki: 0.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.196 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 62.800α = 90.00
b = 62.800β = 90.00
c = 83.500γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1998-09-22 
  • Released Date: 1998-09-30 
  • Deposition Author(s): Ala, P., Chang, C.H.

Revision History 

  • Version 1.0: 1998-09-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations