7KRE

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((6-cyanonaphthalen-1-yl)oxy)-3-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenyl sulfurofluoridate (JLJ704)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Covalent Inhibition of Wild-Type HIV-1 Reverse Transcriptase Using a Fluorosulfate Warhead.

Ippolito, J.A.Niu, H.Bertoletti, N.Carter, Z.J.Jin, S.Spasov, K.A.Cisneros, J.A.Valhondo, M.Cutrona, K.J.Anderson, K.S.Jorgensen, W.L.

(2021) ACS Med Chem Lett 12: 249-255

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00612
  • Primary Citation of Related Structures:  
    7KRC, 7KRD, 7KRE, 7KRF

  • PubMed Abstract: 

    Covalent inhibitors of wild-type HIV-1 reverse transcriptase (CRTIs) are reported. Three compounds derived from catechol diether non-nucleoside inhibitors (NNRTIs) with addition of a fluorosulfate warhead are demonstrated to covalently modify Tyr181 of HIV-RT. X-ray crystal structures for complexes of the CRTIs with the enzyme are provided, which fully demonstrate the covalent attachment, and confirmation is provided by appropriate mass shifts in ESI-TOF mass spectra. The three CRTIs and six noncovalent analogues are found to be potent inhibitors with both IC 50 values for in vitro inhibition of WT RT and EC 50 values for cytopathic protection of HIV-1-infected human T-cells in the 5-320 nM range.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT557Human immunodeficiency virus type 1 BH10Mutation(s): 3 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X2V (Subject of Investigation/LOI)
Query on X2V

Download Ideal Coordinates CCD File 
C [auth A]4-[(6-cyanonaphthalen-1-yl)oxy]-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate
C23 H16 F N3 O7 S
XVIQCYUMLUTRMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.573α = 90
b = 69.554β = 105.9
c = 104.859γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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 StatesAI155072

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description