1QBS

HIV-1 PROTEASE INHIBITORS WIIH LOW NANOMOLAR POTENCY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2' structure-activity relationship, and molecular recognition of cyclic ureas.

Lam, P.Y.Ru, Y.Jadhav, P.K.Aldrich, P.E.DeLucca, G.V.Eyermann, C.J.Chang, C.H.Emmett, G.Holler, E.R.Daneker, W.F.Li, L.Confalone, P.N.McHugh, R.J.Han, Q.Li, R.Markwalder, J.A.Seitz, S.P.Sharpe, T.R.Bacheler, L.T.Rayner, M.M.Klabe, R.M.Shum, L.Winslow, D.L.Kornhauser, D.M.Jackson, D.A.Erickson-Viitanen, S.Hodge, C.N.

(1996) J Med Chem 39: 3514-3525

  • DOI: 10.1021/jm9602571
  • Primary Citation of Related Structures:  
    1QBS

  • PubMed Abstract: 
  • High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptidomimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded to both the mobile flaps of the enzyme and the two carbonyls flanking the transition-state mimic of the inhibitors ...

    High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptidomimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded to both the mobile flaps of the enzyme and the two carbonyls flanking the transition-state mimic of the inhibitors. Using the structure-activity relationships of C2-symmetric diol inhibitors, computed-aided drug design tools, and first principles, we designed and synthesized a novel class of cyclic ureas that incorporates this structural water and preorganizes the side chain residues into optimum binding conformations. Conformational analysis suggested a preference for pseudodiaxial benzylic and pseudodiequatorial hydroxyl substituents and an enantiomeric preference for the RSSR stereochemistry. The X-ray and solution NMR structure of the complex of HIV-1PR and one such cyclic urea, DMP323, confirmed the displacement of the structural water. Additionally, the bound and "unbound" (small-molecule X-ray) ligands have similar conformations. The high degree of preorganization, the complementarity, and the entropic gain of water displacement are proposed to explain the high affinity of these small molecules for the enzyme. The small size probably contributes to the observed good oral bioavailability in animals. Extensive structure-based optimization of the side chains that fill the S2 and S2' pockets of the enzyme resulted in DMP323, which was studied in phase I clinical trials but found to suffer from variable pharmacokinetics in man. This report details the synthesis, conformational analysis, structure-activity relationships, and molecular recognition of this series of C2-symmetry HIV-1PR inhibitors. An initial series of cyclic ureas containing nonsymmetric P2/P2' is also discussed.


    Organizational Affiliation

    DuPont Merck Pharmaceutical Company, DuPont Merck Experimental Station, Wilmington, Delaware 19880-0500, USA. lampy@carbon.dmpc.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 PROTEASEA, B99Human immunodeficiency virus 1Mutation(s): 1 
EC: 3.4.23.16 (PDB Primary Data), 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)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMP
Query on DMP

Download Ideal Coordinates CCD File 
C [auth A][4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE
C35 H38 N2 O5
XCVGQMUMMDXKCY-WZJLIZBTSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
DMP BindingDB:  1QBS Ki: min: 0.27, max: 1 (nM) from 9 assay(s)
Kd: 3.83 (nM) from 1 assay(s)
IC50: min: 15, max: 110 (nM) from 2 assay(s)
Binding MOAD:  1QBS Ki: 0.34 (nM) from 1 assay(s)
PDBBind:  1QBS Ki: 0.34 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • 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: 1997-04-25 
  • Released Date: 1997-10-15 
  • Deposition Author(s): Ala, P., Chang, C.-H.

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-15
    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: 2012-02-22
    Changes: Database references
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other