5C42

Crystal Structure of HIV-1 Reverse Transcriptase (K101P) Variant in Complex with 8-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)indolizine-2-carbonitrile (JLJ555), a non-nucleoside inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance.

Gray, W.T.Frey, K.M.Laskey, S.B.Mislak, A.C.Spasov, K.A.Lee, W.G.Bollini, M.Siliciano, R.F.Jorgensen, W.L.Anderson, K.S.

(2015) Acs Med.Chem.Lett. 6: 1075-1079

  • DOI: 10.1021/acsmedchemlett.5b00254

  • PubMed Abstract: 
  • Catechol diether compounds have nanomolar antiviral and enzymatic activity against HIV with reverse transcriptase (RT) variants containing K101P, a mutation that confers high-level resistance to FDA-approved non-nucleoside inhibitors efavirenz and ri ...

    Catechol diether compounds have nanomolar antiviral and enzymatic activity against HIV with reverse transcriptase (RT) variants containing K101P, a mutation that confers high-level resistance to FDA-approved non-nucleoside inhibitors efavirenz and rilpivirine. Kinetic data suggests that RT (K101P) variants are as catalytically fit as wild-type and thus can potentially increase in the viral population as more antiviral regimens include efavirenz or rilpivirine. Comparison of wild-type structures and a new crystal structure of RT (K101P) in complex with a leading compound confirms that the K101P mutation is not a liability for the catechol diethers while suggesting that key interactions are lost with efavirenz and rilpivirine.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520-8066, United States.,Department of Chemistry, Yale University , New Haven, Connecticut 06530-8107, United States.,Department of Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States ; Howard Hughes Medical Institute , Baltimore, Maryland 21205, United States.,Department of Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Reverse Transcriptase, p66 subunit
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
HIV-1 Reverse Transcriptase, p51 subunit
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
29T
Query on 29T

Download SDF File 
Download CCD File 
A
8-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}indolizine-2-carbonitrile
C21 H16 N4 O4
UUVBMMWJHPNLHN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.244 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 224.198α = 90.00
b = 69.008β = 106.49
c = 104.283γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
HKL-3000data scaling
PHENIXrefinement
PHENIXphasing

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 Diseases (NIH/NIAID)United StatesAI44616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49551
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI104334

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2019-12-11
    Type: Author supporting evidence