6DTW

HIV-1 Reverse Transcriptase Y181C Mutant in complex with JLJ 578


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.742 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular and cellular studies evaluating a potent 2-cyanoindolizine catechol diether NNRTI targeting wildtype and Y181C mutant HIV-1 reverse transcriptase.

Sasaki, T.Gannam, Z.T.K.Kudalkar, S.N.Frey, K.M.Lee, W.G.Spasov, K.A.Jorgensen, W.L.Anderson, K.S.

(2019) Bioorg.Med.Chem.Lett. 29: 2182-2188

  • DOI: 10.1016/j.bmcl.2019.06.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The development of efficacious NNRTIs for HIV/AIDS therapy is commonly met with the emergence of drug resistant strains, including the Y181C variant. Using a computationally-guided approach, we synthesized the catechol diether series of NNRTIs, which ...

    The development of efficacious NNRTIs for HIV/AIDS therapy is commonly met with the emergence of drug resistant strains, including the Y181C variant. Using a computationally-guided approach, we synthesized the catechol diether series of NNRTIs, which display sub-nanomolar potency in cellular assays. Among the most potent were a series of 2-cyanoindolizine substituted catechol diethers, including Compound 1. We present here a thorough evaluation of this compound, including biochemical, cellular, and structural studies. The compound demonstrates low nanomolar potency against both WT and Y181C HIV-1 RT in in vitro and cellular assays. Our crystal structures of both the wildtype and mutant forms of RT in complex with Compound 1 allow the interrogation of this compound's features that allow it to maintain strong efficacy against the drug resistant mutant. Among these are compensatory shifts in the NNRTI binding pocket, persistence of multiple hydrogen bonds, and van der Waals contacts throughout the binding site. Further, the fluorine at the C6 position of the indolizine moiety makes multiple favorable interactions with both RT forms. The present study highlights the indolizine-substituted catechol diether class of NNRTIs as promising therapeutic candidates possessing optimal pharmacological properties and significant potency against multiple RT variants.


    Organizational Affiliation

    Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06520, United States.,Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States.,Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT 06520, United States; Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, United States. Electronic address: karen.anderson@yale.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
557Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 4 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B
428Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 1 
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
H9Y
Query on H9Y

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Download CCD File 
A
8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-6-fluoroindolizine-2-carbonitrile
C21 H14 F2 N4 O4
ZZRRYEXYIVBDNM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.742 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.289α = 90.00
b = 73.899β = 99.50
c = 108.249γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data processing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
Cootmodel building

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 Sciences (NIH/NIGMS)United StatesR01GM049551

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references
  • Version 1.2: 2020-01-01
    Type: Author supporting evidence