2RF2

HIV reverse transcriptase in complex with inhibitor 7e (NNRTI)

• PDB DOI:  https://doi.org/10.2210/pdb2RF2/pdb

• Classification: TRANSFERASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-09-27 Released: 2008-01-01 
• Deposition Author(s): Yan, Y., Prasad, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

Novel indole-3-sulfonamides as potent HIV non-nucleoside reverse transcriptase inhibitors (NNRTIs).

Zhao, Z., Wolkenberg, S.E., Lu, M., Munshi, V., Moyer, G., Feng, M., Carella, A.V., Ecto, L.T., Gabryelski, L.J., Lai, M.T., Prasad, S.G., Yan, Y., McGaughey, G.B., Miller, M.D., Lindsley, C.W., Hartman, G.D., Vacca, J.P., Williams, T.M.

(2008) Bioorg Med Chem Lett 18: 554-559

• PubMed: 18083561 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.085
• Primary Citation of Related Structures:  
  2RF2


• PubMed Abstract: 
  

This Letter describes the design, synthesis, and biological evaluation of novel 3-indole sulfonamides as potent non-nucleoside reverse transcriptase inhibitors (NNRTIs) with balanced profiles against common HIV RT mutants K103N and Y181C.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck & Co., Inc., PO Box 4, West Point, PA 19486, 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 kDa 
• Atom Count: 8,593 
• Modelled Residue Count: 959 
• Deposited Residue Count: 1,006 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)	A	563	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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
Reverse transcriptase/ribonuclease H (EC 2.7.7.49) (EC 2.7.7.7) (EC 3.1.26.4) (p66 RT)	B	443	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRX	C [auth A]	5-bromo-3-(pyrrolidin-1-ylsulfonyl)-1H-indole-2-carboxamide C13 H14 Br N3 O3 S FEPUPYVRZUWCQB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MRX	PDBBind:  2RF2	IC50: 3.6 (nM) from 1 assay(s)
	Binding MOAD:  2RF2	IC50: 3.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.258 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.29	α = 90
b = 155.81	β = 90
c = 155.86	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-01 
Deposition Author(s): Yan, Y., Prasad, S.

Revision History  

• Version 1.0: 2008-01-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description