1HBV

A CHECK ON RATIONAL DRUG DESIGN. CRYSTAL STRUCTURE OF A COMPLEX OF HIV-1 PROTEASE WITH A NOVEL GAMMA-TURN MIMETIC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A check on rational drug design: crystal structure of a complex of human immunodeficiency virus type 1 protease with a novel gamma-turn mimetic inhibitor.

Hoog, S.S.Zhao, B.Winborne, E.Fisher, S.Green, D.W.DesJarlais, R.L.Newlander, K.A.Callahan, J.F.Moore, M.L.Huffman, W.F.Abdel-Meguid, S.S.

(1995) J.Med.Chem. 38: 3246-3252


  • PubMed Abstract: 
  • We have previously reported (Newlander et al., J. Med. Chem. 1993, 36, 2321-2331) the design of human immunodeficiency virus type 1 (HIV-1) protease inhibitors incorporating C7 mimetics that lock three amino acid residues of a peptide sequence into a ...

    We have previously reported (Newlander et al., J. Med. Chem. 1993, 36, 2321-2331) the design of human immunodeficiency virus type 1 (HIV-1) protease inhibitors incorporating C7 mimetics that lock three amino acid residues of a peptide sequence into a gamma-turn. The design of one such compound, SB203238, was based on X-ray structures of reduced amide aspartyl protease inhibitors. It incorporates a gamma-turn mimetic in the P2-P1' position, where the carbonyl of the C7 ring is replaced with an sp3 methylene group yielding a constrained reduced amide. It shows competitive inhibition with Ki = 430 nM at pH 6.0. The three-dimensional structure of SB203238 bound to the active site of HIV-1 protease has been determined at 2.3 A resolution by X-ray diffraction and refined to a crystallographic R-factor (R = sigma magnitude of Fo magnitude of - magnitude of Fc magnitude of /sigma magnitude of Fo magnitude of, where Fo and Fc are the observed and calculated structure factor amplitudes, respectively) of 0.177. The inhibitor lies in an extended conformation in the active site; however, because of the constrained geometry of the C7 ring, it maintains fewer hydrogen bonds with the protein than in most other HIV-1 protease-inhibitor complexes. More importantly, the inhibitor binds to the enzyme differently than predicted in its design, by binding with the P2-P1' alpha-carbon atoms shifted by approximately one-half a residue toward the N-terminus from their presumed positions. This study illustrates the importance of structural information in an approach to rational drug design.


    Related Citations: 
    • A Novel Constrained Reduced-Amide Inhibitor of HIV-1 Protease Derived from the Sequential Incorporation of Gamma-Turn Mimetics Into a Model Substrate
      Newlander, K.A.,Callahan, J.F.,Moore, M.L.,Tomaszek, T.A.,Huffman, W.F.
      (1993) J.Med.Chem. 36: 2321


    Organizational Affiliation

    Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
99Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAN
Query on GAN

Download SDF File 
Download CCD File 
A
2-[3-BENZYL-5-(1-ALANYL-AMINOETHYL)-2,3,6,7-TETRAHYDRO-1H-AZEPIN-1-YL]-1-OXOPROPYL-VALINYL-VALINE-METHYLESTER
C32 H51 N5 O5
AAROLUGLGDXGEZ-CFILSVQKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GANKi: 430 nM BINDINGMOAD
GANKi: 430 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 63.400α = 90.00
b = 63.400β = 90.00
c = 83.900γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORphasing
XENGENdata reduction
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-22
    Type: Database references