8F0F

HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on Darunavir as P2' group

  • Classification: HYDROLASE/INHIBITOR
  • Organism(s): Human immunodeficiency virus 1
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2022-11-02 Released: 2023-02-15 
  • Deposition Author(s): Wang, Y.-F., Agniswamy, J., Ghosh, A.K., Weber, I.T.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Energy (DOE, United States), National Institutes of Health/National Cancer Institute (NIH/NCI), Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Evaluation of darunavir-derived HIV-1 protease inhibitors incorporating P2' amide-derivatives: Synthesis, biological evaluation and structural studies.

Ghosh, A.K.Shahabi, D.Kipfmiller, M.Ghosh, A.K.Johnson, M.Wang, Y.F.Agniswamy, J.Amano, M.Weber, I.T.Mitsuya, H.

(2023) Bioorg Med Chem Lett 83: 129168-129168

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129168
  • Primary Citation of Related Structures:  
    8F0F

  • PubMed Abstract: 

    We report here the synthesis and biological evaluation of darunavir derived HIV-1 protease inhibitors and their functional effect on enzyme inhibition and antiviral activity in MT-2 cell lines. The P2' 4-amino functionality was modified to make a number of amide derivatives to interact with residues in the S2' subsite of the HIV-1 protease active site. Several compounds exhibited picomolar enzyme inhibitory and low nanomolar antiviral activity. The X-ray crystal structure of the chloroacetate derivative bound to HIV-1 protease was determined. Interestingly, the active chloroacetate group converted to the acetate functionality during X-ray exposure. The structure revealed that the P2' carboxamide functionality makes enhanced hydrogen bonding interactions with the backbone atoms in the S2'-subsite.


  • Organizational Affiliation

    Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA. Electronic address: akghosh@purdue.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 5 
Gene Names: pol
EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X7H (Subject of Investigation/LOI)
Query on X7H

Download Ideal Coordinates CCD File 
F [auth B](3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[4-(2-chloroacetamido)benzene-1-sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate
C29 H38 Cl N3 O8 S
WHBOWVZTONSXMQ-NLMMERCGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.133 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.419α = 90
b = 86.235β = 90
c = 46.075γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI150461
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program of the Center for Cancer Research
Japan Agency for Medical Research and Development (AMED)JapanJP15fk0410001
Japan Agency for Medical Research and Development (AMED)JapanJP16fk0410101
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japana Grant-in-Aid for Scientific Research (Priority Areas)

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description