2RKI

Crystal Structure of HIV-1 Reverse Transcriptase (RT) in Complex with a triazole derived NNRTI

• PDB DOI: https://doi.org/10.2210/pdb2RKI/pdb

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


• Deposited: 2007-10-16 Released: 2008-04-22 
• Deposition Author(s): Lansdon, E.B., Kirschberg, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.270 
• R-Value Work: 0.216 

Literature

Triazole derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase-structure-activity relationships and crystallographic analysis.

Kirschberg, T.A., Balakrishnan, M., Huang, W., Hluhanich, R., Kutty, N., Liclican, A.C., McColl, D.J., Squires, N.H., Lansdon, E.B.

(2008) Bioorg Med Chem Lett 18: 1131-1134

• PubMed: 18083512 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.127
• Primary Citation of Related Structures:  
  2RKI


• PubMed Abstract: 
  

  A series of 3,4,5-trisubstituted 1,2,4-4H triazole derivatives was synthesized and investigated for HIV-1 reverse transcriptase inhibition. An X-ray structure with HIV-1 RT secured the binding mode and allowed the key interactions with the enzyme to be identified.

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Organizational Affiliation: 

Gilead Sciences, Department of Medicinal Chemistry, 333 Lakeside Drive, Foster City, CA 94404, USA. [e-mail]

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: 117.13 kDa 
• Atom Count: 8,224 
• Modelled Residue Count: 959 
• Deposited Residue Count: 1,000 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase (RT) p66	A	560	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 reverse transcriptase (RT) p51	B	440	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TT1	C [auth A]	4-benzyl-3-[(2-chlorobenzyl)sulfanyl]-5-thiophen-2-yl-4H-1,2,4-triazole C20 H16 Cl N3 S2 FMDVHVQWAJPVKM-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	J [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	K [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.270 
• R-Value Work: 0.216 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.391	α = 90
b = 154.167	β = 90
c = 154.488	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Lansdon, E.B., Kirschberg, T.A.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description