5UPJ

HIV-2 PROTEASE/U99283 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Use of medium-sized cycloalkyl rings to enhance secondary binding: discovery of a new class of human immunodeficiency virus (HIV) protease inhibitors.

Romines, K.R.Watenpaugh, K.D.Tomich, P.K.Howe, W.J.Morris, J.K.Lovasz, K.D.Mulichak, A.M.Finzel, B.C.Lynn, J.C.Horng, M.-M.Schwende, F.J.Ruwart, M.J.Zipp, G.L.Chong, K.-T.Dolak, L.A.Toth, L.N.Howard, G.M.Rush, B.D.Wilkinson, K.F.Possert, P.L.Dalga, R.J.Hinshaw, R.R.

(1995) J Med Chem 38: 1884-1891

  • DOI: https://doi.org/10.1021/jm00011a008
  • Primary Citation of Related Structures:  
    5UPJ, 6UPJ

  • PubMed Abstract: 

    A unique strategy for the enhancement of secondary binding of an inhibitor to an enzyme has been demonstrated in the design of new human immunodeficiency virus (HIV) protease inhibitors. When the planar benzene ring of a 4-hydroxycoumarin lead compound (1a, Ki = 0.800 microM) was replaced with medium-sized (i.e., 7-9), conformationally-flexible, alkyl rings, the enzyme inhibitory activity of the resulting compounds was dramatically improved, and inhibitors with more than 50-fold better binding (e.g., 5d, Ki = 0.015 microM) were obtained. X-ray crystal structures of these inhibitors complexed with HIV protease indicated the cycloalkyl rings were able to fold into the S1' pocket of the enzyme and fill it much more effectively than the rigid benzene ring of the 4-hydroxycoumarin compound. This work has resulted in the identification of a promising lead structure for the design of potent, deliverable HIV protease inhibitors. Compound 5d, a small (MW = 324), nonpeptidic structure, has already shown several advantages over peptidic inhibitors, including high oral bioavailability (91-99%), a relatively long half-life (4.9 h), and ease of synthesis (three steps).


  • Organizational Affiliation

    Upjohn Laboratories, Kalamazoo, Michigan 49001, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-2 PROTEASE
A, B
99Human immunodeficiency virus 2Mutation(s): 1 
EC: 3.4.23.16
UniProt
Find proteins for P04584 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Explore P04584 
Go to UniProtKB:  P04584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04584
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UIN
Query on UIN

Download Ideal Coordinates CCD File 
C [auth B]5,6,7,8,9,10-HEXAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOOCTA[B]PYRAN-2-ONE
C20 H24 O3
UXCLJNSXDNCIIT-HNNXBMFYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UIN PDBBind:  5UPJ Ki: 75 (nM) from 1 assay(s)
Binding MOAD:  5UPJ Ki: 75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.382α = 90
b = 45.281β = 90
c = 133.359γ = 90
Software Package:
Software NamePurpose
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-22
    Changes: Database references
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations