1B6L

HIV-1 PROTEASE COMPLEXED WITH MACROCYCLIC PEPTIDOMIMETIC INHIBITOR 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/bi990174x
  • Primary Citation of Related Structures:  
    1B6J, 1B6K, 1B6L, 1B6M, 1B6P, 1Z1H, 1Z1R

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RETROPEPSIN
A, B
99Human immunodeficiency virus 1Mutation(s): 0 
EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03369 
Go to UniProtKB:  P03369
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03369
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PI4
Query on PI4

Download Ideal Coordinates CCD File 
E [auth A]1-[2-(8-CARBAMOYLMETHYL-6,9-DIOXO-2-OXA-7,10-DIAZA-BICYCLO[11.2.2]HEPTADECA- 1(16),13(17),14-TRIEN-11-YL)-2-HYDROXY-ETHYL]-PIPERIDINE-2-CARBOXYLIC ACID TERT-BUTYLAMIDE
C28 H43 N5 O6
GHEDXAXQQMZPLE-CWBXHPNXSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ABA
Query on ABA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
Binding Affinity Annotations 
IDSourceBinding Affinity
PI4 Binding MOAD:  1B6L Ki: 5 (nM) from 1 assay(s)
PDBBind:  1B6L Ki: 5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.25α = 90
b = 59.19β = 90
c = 61.76γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-07
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection