1MES

HIV-1 MUTANT (I84V) PROTEASE COMPLEXED WITH DMP323


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors.

Ala, P.J.Huston, E.E.Klabe, R.M.McCabe, D.D.Duke, J.L.Rizzo, C.J.Korant, B.D.DeLoskey, R.J.Lam, P.Y.Hodge, C.N.Chang, C.H.

(1997) Biochemistry 36: 1573-1580

  • DOI: 10.1021/bi962234u
  • Primary Citation of Related Structures:  
    1MEU, 1MET, 1MES, 1MER

  • PubMed Abstract: 
  • In cell cultures, the key residues associated with HIV-1 resistance to cyclic urea-based HIV-1 protease (PR) inhibitors are Val82 and Ile84 of HIV-1 PR. To gain an understanding of how these two residues modulate inhibitor binding, we have measured t ...

    In cell cultures, the key residues associated with HIV-1 resistance to cyclic urea-based HIV-1 protease (PR) inhibitors are Val82 and Ile84 of HIV-1 PR. To gain an understanding of how these two residues modulate inhibitor binding, we have measured the Ki values of three recombinant mutant proteases, I84V, V82F, and V82F/I84V, for DMP323 and DMP450, and determined the three-dimensional structures of their complexes to 2.1-1.9 A resolution with R factors of 18.7-19.6%. The Ki values of these mutants increased by 25-, 0.5-, and 1000-fold compared to the wild-type values of 0.8 and 0.4 nM for DMP323 and DMP450, respectively. The wild-type and mutant complexes overall are very similar (rms deviations of 0.2-0.3 A) except for differences in the patterns of their van der Waals (vdw) interactions, which appear to modulate the Ki values of the mutants. The loss of the CD1 atom of Ile84, in the I84V mutant complexes, creates a hole in the S1 subsite, reducing the number of vdw contacts and increasing the Ki values. The V82F mutant binds DMP323 more tightly than wild type because the side chain of Phe82 forms additional vdw and edge-to-face interactions with the P1 group of DMP323. The Ki values of the single mutants are not additive because the side chain of Phe82 rotates out of the S1 subsite in the double mutant (the chi 1 angles of Phe82 and -182 in the V82F and V82F/I84V mutants differ by 90 and 185 degrees, respectively), further reducing the vdw interactions. Finally, compensatory shifts in the I84V and V82F/ I84V complexes pick up a small number of new contacts, but too few to offset the initial loss of interactions caused by the mutations. Therefore, our data suggest that variants persist in the presence of DMP323 and DMP450 because of a decrease in vdw interactions between the mutant proteases and inhibitors.


    Related Citations: 
    • Erratum. Molecular Basis of HIV-1 Protease Drug Resistance: Structural Analysis of Mutant Proteases Complexed with Cyclic Urea Inhibitors
      Ala, P.J., Huston, E.E., Klabe, R.M., Mccabe, D.D., Duke, J.L., Rizzo, C.J., Korant, B.D., Deloskey, R.J., Lam, P.Y., Hodge, C.N., Chang, C.H.
      (1997) Biochemistry 36: 6556

    Organizational Affiliation

    Department of Chemical and Physical Sciences, DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880-0024, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEAB99Human immunodeficiency virus 1Mutation(s): 1 
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMP
Query on DMP

Download CCD File 
B
[4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE
C35 H38 N2 O5
XCVGQMUMMDXKCY-WZJLIZBTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMPKi:  0.27000001072883606   nM  BindingDB
DMPKi:  1   nM  BindingDB
DMPKi:  20   nM  Binding MOAD
DMPKi :  20   nM  PDBBind
DMPIC50:  15   nM  BindingDB
DMPIC50:  110   nM  BindingDB
DMPKi:  0.3400000035762787   nM  BindingDB
DMPKi:  0.3100000023841858   nM  BindingDB
DMPKi:  0.3199999928474426   nM  BindingDB
DMPKi:  0.27000001072883606   nM  BindingDB
DMPKi:  0.28999999165534973   nM  BindingDB
DMPKi:  0.3100000023841858   nM  BindingDB
DMPKd:  3.8299999237060547   nM  BindingDB
DMPKi:  0.33000001311302185   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.8α = 90
b = 62.8β = 90
c = 83.5γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1997-04-11 
  • Released Date: 1998-04-15 
  • Deposition Author(s): Ala, P., Chang, C.-H.

Revision History 

  • Version 1.0: 1998-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other