6DV4

HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with (R)-Boc-amine and (S)-hydroxyl functionalities as the P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands.

Ghosh, A.K.Jadhav, R.D.Simpson, H.Kovela, S.Osswald, H.Agniswamy, J.Wang, Y.F.Hattori, S.I.Weber, I.T.Mitsuya, H.

(2018) Eur J Med Chem 160: 171-182

  • DOI: 10.1016/j.ejmech.2018.09.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors with carboxamide derivatives as the P2 ligands. We have specifically designed aminothiochromane and aminotetrahydronaphthalene-based carboxami ...

    We describe the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors with carboxamide derivatives as the P2 ligands. We have specifically designed aminothiochromane and aminotetrahydronaphthalene-based carboxamide ligands to promote hydrogen bonding and van der Waals interactions in the active site of HIV-1 protease. Inhibitors 4e and 4j have shown potent enzyme inhibitory and antiviral activity. High resolution X-ray crystal structures of 4d- and 4k-bound HIV-1 protease revealed molecular insights into the ligand-binding site interactions.


    Organizational Affiliation

    Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States. Electronic address: akghosh@purdue.edu.,Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo, 162-8655, Japan; Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto, 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States.,Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA, 30303, United States.,Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States.,Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo, 162-8655, Japan.




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): 5 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GA5
Query on GA5

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B
tert-butyl [(1R,4S)-4-hydroxy-7-{[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamoyl}-1,2,3,4-tetrahydronaphthalen-1-yl]carbamate
C37 H49 N3 O8 S
CBAMANYQGALFBH-ALMGMPQLSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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

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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: 1.14 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.755α = 90.00
b = 86.229β = 90.00
c = 46.181γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

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
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: 2018-10-31
    Type: Initial release