5ULT

HIV-1 wild Type protease with GRL-100-13A (a Crown-like Oxotricyclic Core as the P2-Ligand with the sulfonamide isostere as the P2' group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design and Development of Highly Potent HIV-1 Protease Inhibitors with a Crown-Like Oxotricyclic Core as the P2-Ligand To Combat Multidrug-Resistant HIV Variants.

Ghosh, A.K.Rao, K.V.Nyalapatla, P.R.Osswald, H.L.Martyr, C.D.Aoki, M.Hayashi, H.Agniswamy, J.Wang, Y.F.Bulut, H.Das, D.Weber, I.T.Mitsuya, H.

(2017) J. Med. Chem. 60: 4267-4278

  • DOI: 10.1021/acs.jmedchem.7b00172

  • PubMed Abstract: 
  • Design, synthesis, and evaluation of a new class of exceptionally potent HIV-1 protease inhibitors are reported. Inhibitor 5 displayed superior antiviral activity and drug-resistance profiles. In fact, this inhibitor showed several orders of magnitud ...

    Design, synthesis, and evaluation of a new class of exceptionally potent HIV-1 protease inhibitors are reported. Inhibitor 5 displayed superior antiviral activity and drug-resistance profiles. In fact, this inhibitor showed several orders of magnitude improved antiviral activity over the FDA approved drug darunavir. This inhibitor incorporates an unprecedented 6-5-5 ring-fused crown-like tetrahydropyranofuran as the P2 ligand and an aminobenzothiazole as the P2' ligand with the (R)-hydroxyethylsulfonamide isostere. The crown-like P2 ligand for this inhibitor has been synthesized efficiently in an optically active form using a chiral Diels-Alder catalyst providing a key intermediate in high enantiomeric purity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.


    Organizational Affiliation

    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 BMutation(s): 5 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
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
8FM
Query on 8FM

Download SDF File 
Download CCD File 
B
(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
C30 H40 N2 O8 S
JVINLJIUYCLBEU-JBQMQJJESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.336α = 90.00
b = 86.776β = 90.00
c = 45.252γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXL-97refinement
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 General Medical SciencesUnited StatesGM53386
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM62920
Department of Energy (United States)United StatesW-31-109-Eng-38
National Institutes of HealthUnited Statesthe Intramural Research Program of the Center for Cancer Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanGrant-in-Aid for Scientific Research (Priority Areas)
the Ministry of Health, Welfare, and Labor of JapanJapana Grant for Promotion of AIDS Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanhe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)
Purdue UniversityUnited StatesPurdue University Center for Cancer Research

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Data collection, Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Refinement description