5TER

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile (JLJ651), a Non-nucleoside Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5TER/pdb

• Classification: TRANSFERASE, HYDROLASE/INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-09-22 Released: 2017-01-11 
• Deposition Author(s): Chan, A.H., 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: 2.70 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Starting Model: experimental

Literature

Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents.

Lee, W.G., Chan, A.H., Spasov, K.A., Anderson, K.S., Jorgensen, W.L.

(2016) ACS Med Chem Lett 7: 1156-1160

• PubMed: 27994756 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00390
• Primary Citation of Related Structures:  
  5TER


• PubMed Abstract: 
  

  Catechol diethers that incorporate a 7-cyano-2-naphthyl substituent are reported as non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). Many of the compounds have 1-10 nM potencies toward wild-type HIV-1. An interesting conformational effect allows two unique conformers for the naphthyl group in complexes with HIV-RT. X-ray crystal structures for 4a and 4f illustrate the alternatives.

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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: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 114.6 kDa 
• Atom Count: 7,788 
• Modelled Residue Count: 948 
• 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: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (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 EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.1.13.2 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7AY	C [auth A]	5-chloro-7-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-8-methyl-2-naphthonitrile C24 H18 Cl N3 O4 KFUNYNPQHKSQRQ-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.62	α = 90
b = 74.2	β = 99.98
c = 108.6	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Chan, A.H., 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	GM049551
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI044616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM032136
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI122864

Revision History  

• Version 1.0: 2017-01-11
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description