3GI5

Crystal structure of protease inhibitor, KB62 in complex with wild type HIV-1 protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance.

Nalam, M.N.Ali, A.Altman, M.D.Reddy, G.S.Chellappan, S.Kairys, V.Ozen, A.Cao, H.Gilson, M.K.Tidor, B.Rana, T.M.Schiffer, C.A.

(2010) J.Virol. 84: 5368-5378

  • DOI: 10.1128/JVI.02531-09
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which pre ...

    Drug resistance mutations in HIV-1 protease selectively alter inhibitor binding without significantly affecting substrate recognition and cleavage. This alteration in molecular recognition led us to develop the substrate-envelope hypothesis which predicts that HIV-1 protease inhibitors that fit within the overlapping consensus volume of the substrates are less likely to be susceptible to drug-resistant mutations, as a mutation impacting such inhibitors would simultaneously impact the processing of substrates. To evaluate this hypothesis, over 130 HIV-1 protease inhibitors were designed and synthesized using three different approaches with and without substrate-envelope constraints. A subset of 16 representative inhibitors with binding affinities to wild-type protease ranging from 58 nM to 0.8 pM was chosen for crystallographic analysis. The inhibitor-protease complexes revealed that tightly binding inhibitors (at the picomolar level of affinity) appear to "lock" into the protease active site by forming hydrogen bonds to particular active-site residues. Both this hydrogen bonding pattern and subtle variations in protein-ligand van der Waals interactions distinguish nanomolar from picomolar inhibitors. In general, inhibitors that fit within the substrate envelope, regardless of whether they are picomolar or nanomolar, have flatter profiles with respect to drug-resistant protease variants than inhibitors that protrude beyond the substrate envelope; this provides a strong rationale for incorporating substrate-envelope constraints into structure-based design strategies to develop new HIV-1 protease inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, 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 BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K62
Query on K62

Download SDF File 
Download CCD File 
A
(5S)-3-(3-Acetylphenyl)-N-[(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-2-hydroxy-1-(phenylmethyl)propyl]-2-oxo-5-oxazolidinecarboxamide
(5S)-3-(3-acetylphenyl)-N-{(1S,2R)-3-[(1,3-benzodioxol-5-ylsulfonyl)(2-methylpropyl)amino]-1-benzyl-2-hydroxypropyl}-2-oxo-1,3-oxazolidine-5-carboxamide
C33 H37 N3 O9 S
GNJDFMNCMAQPGN-QXIHQKPUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
K62Ki: 0 - 3.5 nM (100) BINDINGDB
K62Ki: 0.006 nM BINDINGMOAD
K62Ki: 0.006 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.831α = 90.00
b = 58.342β = 90.00
c = 61.629γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description