4KKO

Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 4-((4-methoxy-6-(2-morpholinoethoxy)-1,3,5-triazin-2-yl)amino)-2-((3-methylbut-2-en-1-yl)oxy)benzonitrile (JLJ513), a non-nucleoside inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4KKO/pdb

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


• Deposited: 2013-05-06 Released: 2013-08-14 
• Deposition Author(s): Frey, K.M., Anderson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.289 
• R-Value Work: 0.246 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

Extension into the entrance channel of HIV-1 reverse transcriptase-Crystallography and enhanced solubility.

Bollini, M., Frey, K.M., Cisneros, J.A., Spasov, K.A., Das, K., Bauman, J.D., Arnold, E., Anderson, K.S., Jorgensen, W.L.

(2013) Bioorg Med Chem Lett 23: 5209-5212

• PubMed: 23899617 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.093
• Primary Citation of Related Structures:  
  4KKO, 4KO0


• PubMed Abstract: 
  

  Non-nucleoside inhibitors of HIV-1 reverse transcriptase (HIV-RT) are reported that feature extension into the entrance channel near Glu138. Complexes of the parent anilinylpyrimidine 1 and the morpholinoethoxy analog 2j with HIV-RT have received crystallographic characterization confirming the designs. Measurement of aqueous solubilities of 2j, 2k, the parent triazene 2a, and other NNRTIs demonstrate profound benefits for addition of the morpholinyl substituent.

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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: 114.47 kDa 
• Atom Count: 7,950 
• Modelled Residue Count: 966 
• 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
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: 2.7.7.49
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
1RE	C [auth A]	4-({4-methoxy-6-[2-(morpholin-4-yl)ethoxy]-1,3,5-triazin-2-yl}amino)-2-(3-methylbutoxy)benzonitrile C22 H30 N6 O4 VZBHPTCAQDOYJZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.289 
• R-Value Work: 0.246 
• R-Value Observed: 0.246 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.584	α = 90
b = 73.886	β = 100.16
c = 109.416	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Frey, K.M., Anderson, K.S.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description