2JLE

Novel indazole nnrtis created using molecular template hybridization based on crystallographic overlays

• PDB DOI: https://doi.org/10.2210/pdb2JLE/pdb

• Classification: TRANSFERASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-08 Released: 2009-08-04 
• Deposition Author(s): Jones, L.H., Allan, G., Barba, O., Burt, C., Corbau, R., Dupont, T., Irving, S., Mowbray, C.E., Phillips, C., Swain, N.A., Webster, R., Westby, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.351 (Depositor) 
• R-Value Work: 
  0.261 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.267 (Depositor) 

Literature

Novel Indazole Non-Nucleoside Reverse Transcriptase Inhibitors Using Molecular Hybridization Based on Crystallographic Overlays.

Jones, L.H., Allan, G., Barba, O., Burt, C., Corbau, R., Dupont, T., Knochel, T., Irving, S., Middleton, D.S., Mowbray, C.E., Perros, M., Ringrose, H., Swain, N.A., Webster, R., Westby, M., Phillips, C.

(2009) J Med Chem 52: 1219

• PubMed: 19175319 
• DOI: https://doi.org/10.1021/jm801322h
• Primary Citation of Related Structures:  
  2JLE


• PubMed Abstract: 
  

  A major problem associated with non-nucleoside reverse transcriptase inhibitors (NNRTIs) for the treatment of HIV is their lack of resilience to mutations in the reverse transcriptase (RT) enzyme. Using structural overlays of the known inhibitors efavirenz and capravirine complexed in RT as a starting point, and structure-based drug design techniques, we have created a novel series of indazole NNRTIs that possess excellent metabolic stability and mutant resilience.

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Organizational Affiliation: 

Discovery Chemistry, Sandwich Laboratories, Pfizer Global Research and Development, Ramsgate Road, Sandwich, Kent CT13 9NJ, United Kingdom. [e-mail]

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: 130.74 kDa 
• Atom Count: 8,120 
• Modelled Residue Count: 961 
• Deposited Residue Count: 1,132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REVERSE TRANSCRIPTASE/RNASEH	A, B	566	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q72547 (Human immunodeficiency virus type 1) Explore Q72547  Go to UniProtKB:  Q72547

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I15	C [auth A]	5-[(5-fluoro-3-methyl-1H-indazol-4-yl)oxy]benzene-1,3-dicarbonitrile C16 H9 F N4 O JYAHFMKZJRVTDT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I15	BindingDB:  2JLE	IC50: min: 50, max: 384 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.351 (Depositor) 
• R-Value Work:  0.261 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.267 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.2	α = 90
b = 154.6	β = 90
c = 155	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Jones, L.H., Allan, G., Barba, O., Burt, C., Corbau, R., Dupont, T., Irving, S., Mowbray, C.E., Phillips, C., Swain, N.A., Webster, R., Westby, M.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other