3MXE

Crystal structure of HIV-1 protease inhibitor, KC32 complexed with wild-type protease

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure-Based Design, Synthesis, and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones.

Ali, A., Reddy, G.S., Nalam, M.N., Anjum, S.G., Cao, H., Schiffer, C.A., Rana, T.M.

(2010) J.Med.Chem. 53: 7699-7708

  • DOI: 10.1021/jm1008743
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • A series of new HIV-1 protease inhibitors with the hydroxyethylamine core and different phenyloxazolidinone P2 ligands were designed and synthesized. Variation of phenyl substitutions at the P2 and P2' moieties significantly affected the binding affi ...

    A series of new HIV-1 protease inhibitors with the hydroxyethylamine core and different phenyloxazolidinone P2 ligands were designed and synthesized. Variation of phenyl substitutions at the P2 and P2' moieties significantly affected the binding affinity and antiviral potency of the inhibitors. In general, compounds with 2- and 4-substituted phenyloxazolidinones at P2 exhibited lower binding affinities than 3-substituted analogues. Crystal structure analyses of ligand-enzyme complexes revealed different binding modes for 2- and 3-substituted P2 moieties in the protease S2 binding pocket, which may explain their different binding affinities. Several compounds with 3-substituted P2 moieties demonstrated picomolar binding affinity and low nanomolar antiviral potency against patient-derived viruses from HIV-1 clades A, B, and C, and most retained potency against drug-resistant viruses. Further optimization of these compounds using structure-based design may lead to the development of novel protease inhibitors with improved activity against drug-resistant strains of HIV-1.

    Organizational Affiliation: 

    University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)Mutation(s): 2 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K54
Query on K54
Download SDF File 
Download CCD File 
A
(5S)-N-{(1S,2R)-3-[(1,3-benzothiazol-6-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-2-oxo-3-[2-(trifluoromethyl)phenyl]-1,3-oxazolidine-5-carboxamide
(5S)-N-[(1S,2R)-3-[(6-Benzothiazolylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)propyl]-2-oxo-3-[2-(trifluoromethyl)phenyl]oxazolidine-5-carboxamide
C32 H33 F3 N4 O6 S2
NMADTNHSJGJGDP-ITHJLQSDSA-N
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K54Ki: 0.097 nM BINDINGMOAD
K54Ki: 0.097 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.790α = 90.00
b = 58.245β = 90.00
c = 62.014γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description