5UPZ

HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with the para-hydoxymethyl sulfonamide isostere as the P2' group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 Ki of 0.025nM and antiviral IC50 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 Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA. Electronic address: akghosh@purdue.edu.




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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8HD
Query on 8HD

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Download CCD File 
A
N~3~-{(2S,3R)-3-hydroxy-4-[{[4-(hydroxymethyl)phenyl]sulfonyl}(2-methylpropyl)amino]-1-phenylbutan-2-yl}-N~1~-methyl-N~1~-[(4-methyl-1,3-oxazol-2-yl)methyl]benzene-1,3-dicarboxamide
C35 H42 N4 O7 S
PQWSVCGBIGOYSI-AJQTZOPKSA-N
 Ligand Interaction
NA
Query on NA

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

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.27 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.175α = 90.00
b = 86.418β = 90.00
c = 45.828γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
SHELXL-97refinement

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 StatesNo. W-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)
he 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