1HVR

RATIONAL DESIGN OF POTENT, BIOAVAILABLE, NONPEPTIDE CYCLIC UREAS AS HIV PROTEASE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors.

Lam, P.Y.Jadhav, P.K.Eyermann, C.J.Hodge, C.N.Ru, Y.Bacheler, L.T.Meek, J.L.Otto, M.J.Rayner, M.M.Wong, Y.N.Chang, C.-H.Weber, P.Jackson, D.A.Sharpe, T.R.Erickson-Viitanen, S.

(1994) Science 263: 380-384

  • DOI: 10.1126/science.8278812
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule ...

    Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule. The success of the design in both displacing and mimicking the structural water molecule was confirmed by x-ray crystallographic studies. Highly selective, preorganized inhibitors with relatively low molecular weight and high oral bioavailability were synthesized.


    Organizational Affiliation

    Department of Virology Research, DuPont Merck Pharmaceutical Company, Wilmington, DE 19880.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XK2
Query on XK2

Download CCD File 
A
[4R-(4ALPHA,5ALPHA,6BETA,7BETA)]-HEXAHYDRO-5,6-DIHYDROXY-1,3-BIS[2-NAPHTHYL-METHYL]-4,7-BIS(PHENYLMETHYL)-2H-1,3-DIAZEPIN-2-ONE
C41 H38 N2 O3
VUYPJDFAKYXJEV-WESAGZJESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XK2Ki:  0.3100000023841858   nM  Binding MOAD
XK2Ki :  0.3100000023841858   nM  PDBBind
XK2Ki:  0.3100000023841858   nM  BindingDB
XK2Ki:  0.3100000023841858   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.8α = 90
b = 62.8β = 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

  • Deposited Date: 1994-02-14 
  • Released Date: 1995-01-26 
  • Deposition Author(s): Chang, C.-H.

Revision History 

  • Version 1.0: 1995-01-26
    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: 2012-02-29
    Changes: Database references
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other