1Z1H

HIV-1 protease complexed with macrocyclic peptidomimetic inhibitor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease

Martin, J.L.Begun, J.Schindeler, A.Wickramasinghe, W.A.Alewood, D.Alewood, P.F.Bergman, D.A.Brinkworth, R.I.Abbenante, G.March, D.R.Reid, R.C.Fairlie, D.P.

(1999) Biochemistry 38: 7978-7988

  • DOI: 10.1021/bi990174x
  • Primary Citation of Related Structures:  
  • Also Cited By: 3BXS, 3BXR

  • PubMed Abstract: 
  • High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from p ...

    High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a beta-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 A N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba67,95]HIVPR and [Lys7,Ile33,Aba67,95]HIVPR used in this work were shown to have very similar crystal structures.


    Organizational Affiliation

    Centre for Drug Design and Development, University of Queensland, Brisbane QLD 4072, Australia. j.martin@mailbox.uq.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pol polyprotein
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 4 
Gene Names: gag-pol
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03369
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HBB
Query on HBB

Download SDF File 
Download CCD File 
A
N-{(2R)-2-HYDROXY-2-[(8S,11S)-8-ISOPROPYL-6,9-DIOXO-2-OXA-7,10-DIAZABICYCLO[11.2.2]HEPTADECA-1(15),13,16-TRIEN-11-YL]ETHYL}-N-ISOPENTYLBENZENESULFONAMIDE
N-[2-HYDROXY-2-(8-ISOPROPYL-6,9-DIOXO-2-OXA-7,10-DIAZA-BICYCLO[11.2.2]HEPTADECA-1(16),13(17),14-TRIEN-11-YL)-ETHYL]-N-(3-METHYL-BUTYL)-BENZENESULFONAMIDE, INHIBITOR 3
C30 H43 N3 O6 S
WRUVOSYKHXGAQN-GKRYNVPLSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBBKi: 4 nM (89) BINDINGDB
HBBKi: 4 nM BINDINGMOAD
HBBKi: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.400α = 90.00
b = 59.000β = 90.00
c = 62.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance