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)

• PDB DOI: https://doi.org/10.2210/pdb7KRE/pdb

• Classification: TRANSFERASE, Hydrolase/Inhibitor
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-11-19 Released: 2021-01-13 
• Deposition Author(s): Bertoletti, N., Ippolito, J.A., Jorgensen, W.L., Anderson, K.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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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

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

• PubMed: 33603971 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.53 kDa 
• Atom Count: 7,482 
• Modelled Residue Count: 940 
• Deposited Residue Count: 985 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE, P66 SUBUNIT	A	557	Human immunodeficiency virus type 1 BH10	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 REVERSE TRANSCRIPTASE, P51 SUBUNIT	B	428	Human immunodeficiency virus type 1 BH10	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X2V (Subject of Investigation/LOI)	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 = 226.573	α = 90
b = 69.554	β = 105.9
c = 104.859	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Bertoletti, N., Ippolito, J.A., Jorgensen, W.L., Anderson, K.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49551
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI155072

Revision History  

• 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