1HWR

MOLECULAR RECOGNITION OF CYCLIC UREA HIV PROTEASE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular recognition of cyclic urea HIV-1 protease inhibitors.

Ala, P.J.DeLoskey, R.J.Huston, E.E.Jadhav, P.K.Lam, P.Y.Eyermann, C.J.Hodge, C.N.Schadt, M.C.Lewandowski, F.A.Weber, P.C.McCabe, D.D.Duke, J.L.Chang, C.H.

(1998) J Biol Chem 273: 12325-12331

  • DOI: https://doi.org/10.1074/jbc.273.20.12325
  • Primary Citation of Related Structures:  
    1HWR

  • PubMed Abstract: 

    As long as the threat of human immunodeficiency virus (HIV) protease drug resistance still exists, there will be a need for more potent antiretroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new interactions that might improve their therapeutic benefit. The structures reveal that the preorganized, C2 symmetric scaffolds of the inhibitors are anchored in the active site of the protease by six hydrogen bonds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibitors possess benzyl groups at P1 and P1', their relative binding affinities are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (Ki (inhibition constant) = 4.70 nM), possesses the smallest P2 and the lowest number of P2-S2 interactions; whereas SD146, the most potent inhibitor (Ki = 0.02 nM), contains a benzimidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and approximately 200 van der Waals interactions. This analysis identifies the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral protease increase the binding affinity of HIV protease inhibitors.


  • Organizational Affiliation

    DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
216
Query on 216

Download Ideal Coordinates CCD File 
C [auth B][4-R-(4-ALPHA,6-BETA,7-BETA]-HEXAHYDRO-5,6-DI(HYDROXY)-1,3-DI(ALLYL)-4,7-BISPHENYLMETHYL)-2H-1,3-DIAZEPINONE
C25 H30 N2 O3
IWJSQELMWLOYSO-LWSSLDFYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
216 Binding MOAD:  1HWR Ki: 4.7 (nM) from 1 assay(s)
BindingDB:  1HWR Ki: min: 4.6, max: 5.2 (nM) from 4 assay(s)
PDBBind:  1HWR Ki: 4.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.9α = 90
b = 62.9β = 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

  • Released Date: 1999-03-23 
  • Deposition Author(s): Chang, C.-H.

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-23
    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
  • Version 1.4: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description