5C25

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 6-((4-((4-cyanophenyl)amino)-1,3,5-triazin-2-yl)amino)-5,7-dimethyl-2-naphthonitrile (JLJ639), a Non-nucleoside Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5C25/pdb

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


• Deposited: 2015-06-15 Released: 2015-07-29 
• Deposition Author(s): Chan, A.H., Frey, K.M., Anderson, K.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase.

Lee, W.G., Frey, K.M., Gallardo-Macias, R., Spasov, K.A., Chan, A.H., Anderson, K.S., Jorgensen, W.L.

(2015) Bioorg Med Chem Lett 25: 4824-4827

• PubMed: 26166629 
• DOI: https://doi.org/10.1016/j.bmcl.2015.06.074
• Primary Citation of Related Structures:  
  5C24, 5C25


• PubMed Abstract: 
  

  Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that incorporate a 7-indolizinylamino or 2-naphthylamino substituent on a pyrimidine or 1,3,5-triazine core. The most potent compounds show below 10 nanomolar activity towards wild-type HIV-1 and variants bearing Tyr181Cys and Lys103Asn/Tyr181Cys resistance mutations. The compounds also feature good aqueous solubility. Crystal structures for two complexes enhance the analysis of the structure-activity data.

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Organizational Affiliation: 

Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.

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: 114.64 kDa 
• Atom Count: 7,897 
• Modelled Residue Count: 960 
• 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)
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)
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
639	C [auth A]	6-({4-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}amino)-5,7- dimethyl-2-naphthonitrile C23 H17 N7 KPKGAKOSWKZAAI-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.263 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.15785/SBGRID/168

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.554	α = 90
b = 72.969	β = 100.66
c = 109.479	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Chan, A.H., Frey, K.M., Anderson, K.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI27690
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI44616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM32136
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	AI104334

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description