HIV-1 Protease NL4-3 WT in Complex with LR2-21

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope.

Rusere, L.N.Lockbaum, G.J.Lee, S.K.Henes, M.Kosovrasti, K.Spielvogel, E.Nalivaika, E.A.Swanstrom, R.Yilmaz, N.K.Schiffer, C.A.Ali, A.

(2019) J Med Chem 62: 8062-8079

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00838
  • Primary Citation of Related Structures:  
    6OXO, 6OXP, 6OXQ, 6OXR, 6OXS, 6OXT, 6OXU, 6OXV, 6OXW, 6OXX, 6OXY, 6OXZ, 6OY0, 6OY1, 6OY2

  • PubMed Abstract: 

    A structure-guided design strategy was used to improve the resistance profile of HIV-1 protease inhibitors by optimizing hydrogen bonding and van der Waals interactions with the protease while staying within the substrate envelope. Stereoisomers of 4-(1-hydroxyethyl)benzene and 4-(1,2-dihydroxyethyl)benzene moieties were explored as P2' ligands providing pairs of diastereoisomers epimeric at P2', which exhibited distinct potency profiles depending on the configuration of the hydroxyl group and size of the P1' group. While compounds with the 4-(1-hydroxyethyl)benzene P2' moiety maintained excellent antiviral potency against a panel of multidrug-resistant HIV-1 strains, analogues with the polar 4-(1,2-dihydroxyethyl)benzene moiety were less potent, and only the ( R )-epimer incorporating a larger 2-ethylbutyl P1' group showed improved potency. Crystal structures of protease-inhibitor complexes revealed strong hydrogen bonding interactions of both ( R )- and ( S )-stereoisomers of the hydroxyethyl group with Asp30'. Notably, the ( R )-dihydroxyethyl group was involved in a unique pattern of direct hydrogen bonding interactions with the backbone amides of Asp29' and Asp30'. The SAR data and analysis of crystal structures provide insights for optimizing these promising HIV-1 protease inhibitors.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease NL4-3A [auth B],
B [auth A]
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NJ7 (Subject of Investigation/LOI)
Query on NJ7

Download Ideal Coordinates CCD File 
F [auth A](3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{({4-[(1S)-1,2-dihydroxyethyl]phenyl}sulfonyl)[(2S)-2-methylbutyl]amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate
C30 H42 N2 O9 S
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A],
E [auth A]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.084α = 90
b = 58.123β = 90
c = 62.325γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01-GM109767

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description