5YOK

Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine.

Hidaka, K.Kimura, T.Sankaranarayanan, R.Wang, J.McDaniel, K.F.Kempf, D.J.Kameoka, M.Adachi, M.Kuroki, R.Nguyen, J.T.Hayashi, Y.Kiso, Y.

(2018) J. Med. Chem. 61: 5138-5153

  • DOI: 10.1021/acs.jmedchem.7b01709
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based p ...

    The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based peptidomimetics with various P 3 , P 2 , and P 2 ́ moieties. The derivatives with P 2 tetrahydrofuranylglycine (Thfg) were found to be potent against wild type HIV-1 protease and the virus, leading to a highly potent compound 21f (KNI-1657) against lopinavir/ritonavir- or darunavir-resistant strains. Co-crystal structures of 21f and the wild-type protease revealed numerous key hydrogen bonding interactions with Thfg. These results suggest that the strategy to design allophenylnorstatine-based peptidomimetics combined with Thfg residue would be promising for generating candidates to overcome multidrug resistance.


    Organizational Affiliation

    Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical Sciences , Kobe Gakuin University , Kobe 650-8586 , Japan.,Laboratory of Peptide Sciences , Nagahama Institute of Bio-Science and Technology , Nagahama 526-0829 , Japan.,Department of Medicinal Chemistry , Tokyo University of Pharmacy and Life Sciences , Tokyo 192-0392 , Japan.,Department of Medicinal Chemistry , Kyoto Pharmaceutical University , Kyoto 607-8412 , Japan.,Quantum Beam Science Center , Japan Atomic Energy Agency , Tokai , Ibaraki 319-1195 , Japan.,Global Pharmaceutical Research and Development , AbbVie , North Chicago , Illinois 60064 , United States.,Quantum Beam Science Drectorate , National Institutes for Quantum and Radiological Science and Technology , Tokai , Ibaraki 319-1106 , Japan.,Department of International Health , Kobe University Graduate School of Health Sciences , Kobe 654-0142 , Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 PROTEASE
A, B
100Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
Go to UniProtKB:  P03367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
8Z0
Query on 8Z0

Download SDF File 
Download CCD File 
A
(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofuran-2-yl)carbonylamino]-2-[(3R)-oxolan-3-yl]ethanoyl]amino]-2-oxidanyl-4-phenyl-butanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
KNI-1657
C41 H48 N4 O8 S
ZNVSERMHCCYPMY-JZILQDPNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.125 
  • R-Value Work: 0.103 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.250α = 90.00
b = 85.948β = 90.00
c = 46.529γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
SCALAdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release