3O9G

Crystal Structure of wild-type HIV-1 Protease in complex with af53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance.

Nalam, M.N.Ali, A.Reddy, G.S.Cao, H.Anjum, S.G.Altman, M.D.Yilmaz, N.K.Tidor, B.Rana, T.M.Schiffer, C.A.

(2013) Chem.Biol. 20: 1116-1124

  • DOI: 10.1016/j.chembiol.2013.07.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibito ...

    The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against different clades of HIV as well as a panel of 12 drug-resistant viral strains. The substrate envelope model proves to be a powerful strategy to develop potent and robust inhibitors that avoid drug resistance.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Go to UniProtKB:  P03369
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
F53
Query on F53

Download SDF File 
Download CCD File 
A
(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-3-[(2-ethylbutyl){[4-(hydroxymethyl)phenyl]sulfonyl}amino]-2-hydroxypropyl}carbamate
C30 H42 N2 O8 S
KOYHHSRUNXTXFB-WNJKUOTESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F53Ki: 0 - 0.1 nM (88) BINDINGDB
F53Ki: 0.0005 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.675α = 90.00
b = 57.816β = 90.00
c = 61.741γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Refinement description
  • Version 1.2: 2011-11-23
    Type: Structure summary
  • Version 1.3: 2013-11-27
    Type: Database references
  • Version 1.4: 2014-03-19
    Type: Other
  • Version 1.5: 2017-11-08
    Type: Refinement description