6UPJ

HIV-2 PROTEASE/U99294 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • Primary Citation of Related Structures:  

  • 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 compou ...

    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).


    Related Citations: 
    • Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors.
      Skulnick, H.I.,Johnson, P.D.,Howe, W.J.,Tomich, P.K.,Chong, K.-T.,Watenpaugh, K.D.,Janakiraman, M.N.,Dolak, L.A.,Mcgrath, J.P.,Lynn, J.C.,Horng, M.-M.,Hinshaw, R.R.,Zipp, G.L.,Ruwart, M.J.,Schwende, F.J.,Zhong, W.-Z.,Padbury, G.E.,Dalga, R.J.,Shiou, L.,Possert, P.L.,Rush, B.D.,Wilkinson, K.F.,Howard, G.M.,Toth, L.N.,Williams, M.G.,Kakuk, T.J.,Cole, S.L.,Zaya, R.M.,Lovasz, K.D.,Morris, J.K.,Romines, K.R.,Thaisrivongs, S.,Aristoff, P.A.
      (1995) J.Med.Chem. 38: 4968


    Organizational Affiliation

    Upjohn Laboratories, Kalamazoo, Michigan 49001, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-2 PROTEASE
A, B
99Human immunodeficiency virus type 2 subtype A (isolate ROD)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04584 (Human immunodeficiency virus type 2 subtype A (isolate ROD))
Go to UniProtKB:  P04584
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIU
Query on NIU

Download SDF File 
Download CCD File 
A
6,7,8,9-TETRAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOHEPTA[B]PYRAN-2-ONE
C19 H22 O3
YKJXQZGJGDTEOC-AWEZNQCLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NIUKi: 480 nM BINDINGMOAD
NIUKi: 480 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.889α = 90.00
b = 45.675β = 90.00
c = 134.574γ = 90.00
Software Package:
Software NamePurpose
XENGENdata reduction
CEDARrefinement
XENGENdata scaling
MERLOTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references