3C6U

Crystal Structure of HIV Reverse Transcriptase in complex with inhibitor 22

• PDB DOI: https://doi.org/10.2210/pdb3C6U/pdb

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


• Deposited: 2008-02-05 Released: 2008-04-22 
• Deposition Author(s): Yan, Y., Prasad, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

The design and synthesis of diaryl ether second generation HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) with enhanced potency versus key clinical mutations.

Tucker, T.J., Saggar, S., Sisko, J.T., Tynebor, R.M., Williams, T.M., Felock, P.J., Flynn, J.A., Lai, M.T., Liang, Y., McGaughey, G., Liu, M., Miller, M., Moyer, G., Munshi, V., Perlow-Poehnelt, R., Prasad, S., Sanchez, R., Torrent, M., Vacca, J.P., Wan, B.L., Yan, Y.

(2008) Bioorg Med Chem Lett 18: 2959-2966

• PubMed: 18396399 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.064
• Primary Citation of Related Structures:  
  3C6T, 3C6U


• PubMed Abstract: 
  

  Using a combination of traditional Medicinal Chemistry/SAR analysis, crystallography, and molecular modeling, we have designed and synthesized a series of novel, highly potent NNRTIs that possess broad antiviral activity against a number of key clinical mutations.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, WP14-3, 770 Sumneytown Pike, PO Box 4, West Point, PA 19486-0004, 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: 117.04 kDa 
• Atom Count: 8,289 
• Modelled Residue Count: 962 
• Deposited Residue Count: 1,006 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase	A	563	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data)
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	B	443	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol
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
M22	C [auth A]	3-chloro-5-[2-chloro-5-(1H-indazol-3-ylmethoxy)phenoxy]benzonitrile C21 H13 Cl2 N3 O2 WHCLIFOVZDANCU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M22	BindingDB:  3C6U	IC50: min: 1.1, max: 2.6 (nM) from 3 assay(s)
	PDBBind:  3C6U	IC50: 1.35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.75	α = 90
b = 154.2	β = 90
c = 156.15	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Yan, Y., Prasad, S.

Revision History  

• Version 1.0: 2008-04-22
  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