3T19

Crystal structure of HIV-1 reverse transcriptase (wild type) in complex with inhibitor M05


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and synthesis of conformationally constrained inhibitors of non-nucleoside reverse transcriptase.

Gomez, R.Jolly, S.J.Williams, T.Vacca, J.P.Torrent, M.McGaughey, G.Lai, M.T.Felock, P.Munshi, V.Distefano, D.Flynn, J.Miller, M.Yan, Y.Reid, J.Sanchez, R.Liang, Y.Paton, B.Wan, B.L.Anthony, N.

(2011) J.Med.Chem. 54: 7920-7933

  • DOI: 10.1021/jm2010173
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Highly active antiretroviral therapy (HAART) significantly reduces human immunodeficiency virus (HIV) viral load and has led to a dramatic decrease in acquired immunodeficiency syndrome (AIDS) related mortality. Despite this success, there remains a ...

    Highly active antiretroviral therapy (HAART) significantly reduces human immunodeficiency virus (HIV) viral load and has led to a dramatic decrease in acquired immunodeficiency syndrome (AIDS) related mortality. Despite this success, there remains a critical need for new HIV therapies to address the emergence of drug resistant viral strains. Next generation NNRTIs are sought that are effective against these mutant forms of the HIV virus. The bound conformations of our lead inhibitors, MK-1107 (1) and MK-4965 (2), were divergent about the oxymethylene linker, and each of these conformations was rigidified using two isomeric cyclic constraints. The constraint derived from the bioactive conformation of 2provided novel, highly potent NNRTIs that possess broad spectrum antiviral activity and good pharmacokinetic profiles. Systematic SAR led to the identification of indazole as the optimal conformational constraint to provide MK-6186 (3) and MK-7445 (6). Despite their reduced flexibility, these compounds had potency comparable to that of the corresponding acyclic ethers in both recombinant enzyme and cell based assays against both the wild-type and the clinically relevant mutant strains.


    Organizational Affiliation

    Departments of West Point Discovery Chemistry, Pennsylvania 19486-0004, United States. Robert_gomez@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse Transcriptase
A, B
563Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5MA
Query on 5MA

Download SDF File 
Download CCD File 
A
1-(2,5-dichloro-3-{[5-chloro-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1H-benzotriazol-4-yl]oxy}phenyl)methanamine
C20 H14 Cl3 N7 O
CUYHWBGVPXGMKQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5MAKi: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.060α = 90.00
b = 153.660β = 90.00
c = 154.880γ = 90.00
Software Package:
Software NamePurpose
BUSTERphasing
ADSCdata collection
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-21 
  • Released Date: 2011-10-26 
  • Deposition Author(s): Yan, Y., Reid, J.

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references