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 
  • R-Value Observed: 0.182 

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:  
    1Z1H, 1Z1R, 1B6L, 1B6K, 1B6J, 1B6P, 1B6M

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pol polyproteinAB99N/AMutation(s): 4 
EC: 3.4.23.16
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBB
Query on HBB

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
C30 H43 N3 O6 S
WRUVOSYKHXGAQN-GKRYNVPLSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
A,BL-PEPTIDE LINKINGC4 H9 N O2ALA
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBBKi:  4   nM  Binding MOAD
HBBKi:  4   nM  BindingDB
HBBKi :  4   nM  PDBBind
HBBKi:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.4α = 90
b = 59β = 90
c = 62γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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