6E7J

HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold as the P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies.

Ghosh, A.K.Williams, J.N.Ho, R.Y.Simpson, H.M.Hattori, S.I.Hayashi, H.Agniswamy, J.Wang, Y.F.Weber, I.T.Mitsuya, H.

(2018) J. Med. Chem. 61: 9722-9737

  • DOI: 10.1021/acs.jmedchem.8b01227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a ...

    We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a key o-iodoxybenzoic acid mediated cyclization. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Compound 4k has shown an enzyme K i of 40 pM and antiviral IC 50 of 31 nM. Inhibitors 4k and 4l were evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants, and their fold-changes in antiviral activity were similar to those observed with darunavir. Additionally, two X-ray crystal structures of the related inhibitors 4a and 4e bound to HIV-1 protease were determined at 1.22 and 1.30 Å resolution, respectively, and revealed important interactions in the active site that have not yet been explored.


    Organizational Affiliation

    Departments of Infectious Diseases and Hematology , Kumamoto University Graduate School of Biomedical Sciences , Kumamoto 860-8556 , Japan.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch , National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States.,Department of Biology, Molecular Basis of Disease , Georgia State University , Atlanta , Georgia 30303 , United States.,Department of Refractory Viral Infections , National Center for Global Health and Medicine Research Institute , Tokyo 162-8655 , Japan.,Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HWY
Query on HWY

Download SDF File 
Download CCD File 
A
(3aS,5R,6aR)-2-oxo-3-phenylhexahydro-2H-cyclopenta[d][1,3]oxazol-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
C34 H41 N3 O8 S
MCFYAJCOYWLLEO-YGMVDIOKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.793α = 90.00
b = 86.043β = 90.00
c = 45.875γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesGM53386
National Institutes of Health/National Cancer InstituteUnited StatesGM62920
National Institutes of Health/National Cancer InstituteUnited Statesthe Intramural Research Program of the Center for Cancer Research
Department of Energy (United States)United StatesW-31-109-Eng-38
National Institutes of Health/National Cancer InstituteUnited Statesthe Intramural Research Program of the Center for Cancer Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japana Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanthe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Refinement description