5UOV

HIV-1 wild Type protease with GRL-1118A , an isophthalamide-derived P2-P3 ligand with the sulfonamide isostere as the P2' group

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex.

Ghosh, A.K., Brindisi, M., Nyalapatla, P.R., Takayama, J., Ella-Menye, J.R., Yashchuk, S., Agniswamy, J., Wang, Y.F., Aoki, M., Amano, M., Weber, I.T., Mitsuya, H.

(2017) Bioorg. Med. Chem. 25: 5114-5127

  • DOI: 10.1016/j.bmc.2017.04.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands ...

    Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands for specific interactions in the S2-S3 extended site. Compound 4b has shown an enzyme K i of 0.025nM and antiviral IC 50 of 69nM. An X-ray crystal structure of inhibitor 4b-HIV-1 protease complex was determined at 1.33Å resolution. We have also determined X-ray structure of 3b-bound HIV-1 protease at 1.27Å resolution. These structures revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site.

    Organizational Affiliation: 

    Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.,Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA. Electronic address: akghosh@purdue.edu.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.,Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Department of Refractory Viral Infection, National Center for Global Health and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan.,Department of Biology, Georgia State University, Atlanta, GA 30303, USA.




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 BH10)Mutation(s): 5 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 5 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
ACT
Query on ACT
Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8FP
Query on 8FP
Download SDF File 
Download CCD File 
A
N-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-3-[(2R)-2-(4-methyl-1,3-thiazol-2-yl)pyrrolidine-1-carbonyl]benzamide
C37 H44 N4 O6 S2
ZHCCHBWXFODCGA-LBFZIJHGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8FPKi: 0.025 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.179α = 90.00
b = 86.515β = 90.00
c = 45.945γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXL-97refinement
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM53386
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM62920
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38
National Institutes of Health/National Cancer Institute (NIH/NCI)United 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 Health, Welfare, and LaborJapana Grant for Promotion of AIDS Research
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)
Purdue UniversityUnited Statesthe Purdue University Center for Cancer Research

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence
  • Version 1.2: 2017-10-04
    Type: Database references
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence