9OBI | pdb_00009obi

Room Temperature X-Ray Structure of HIV-1 Protease in Complex with Inhibitor GRL-075-24A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.198 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.168 (Depositor) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Literature

Design, synthesis, evaluation and X-ray structural studies of potent HIV-1 protease inhibitors containing substituted oxaspirocyclic carbamates as the P2 ligands.

Ghosh, A.K.Shaktah, R.Ghosh, A.K.Johnson, M.E.Bhandari, D.Amano, M.Aoki, M.Kovalevsky, A.Mitsuya, H.

(2025) Eur J Med Chem 297: 117880-117880

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117880
  • Primary Citation Related Structures: 
    9OBI

  • PubMed Abstract: 

    We report here the design, synthesis and evaluation of a series of HIV-1 protease inhibitors that incorporate substituted oxaspirocyclic carbamate derivatives to serve as the P2 ligands. Various substituted ligand derivatives were synthesized in a racemic manner, using a tandem Prins/pinacol reaction as the key reaction. This reaction sets the relative stereochemistry of the oxaspirocyclic template in a highly diastereoselective manner. Reaction of the resulting ketone with enantiopure (S)-tert-butyl sulfinamide provided a convenient pathway to resolve the oxaspirocyclic ketone derivatives. The absolute stereochemical identity was determined by X-ray crystallography. The structure-activity studies demonstrate the effect of the stereochemistry of the oxaspirocyclic ring systems as well as the substitution effect on the aromatic ring. Several inhibitors exhibited potent HIV-1 protease inhibitory activity. One of these inhibitors displayed subnanomolar HIV-1 protease affinity and also exhibited potent antiviral activity. A high-resolution X-ray crystal structure of this inhibitor-bound HIV-1 protease show that the oxaspirocyclic P2 ligand forms an unconventional C-H⋯O bond with the backbone carboxyl group of Gly48' and an interesting N-H … π interaction with the aromatic ring in the S2 subsite of HIV-1 protease active site.


  • Organizational Affiliation
    • Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA. Electronic address: akghosh@purdue.edu.

Macromolecule Content 

  • Total Structure Weight: 88.78 kDa 
  • Atom Count: 6,817 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 792 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protease
A, B, C, D, E
A, B, C, D, E, F, G, H
99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
EC: 3.4.23.16
UniProt
Find proteins for Q7SSI0 (Human immunodeficiency virus type 1)
Explore Q7SSI0 
Go to UniProtKB:  Q7SSI0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SSI0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.198 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.168 (Depositor) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.088α = 90
b = 69.487β = 90.06
c = 89.433γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI150466

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release