3T1A

Crystal Structure of HIV-1 Reverse Transcriptase (K103N mutant) in Complex with Inhibitor M05


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jm2010173
  • Primary Citation of Related Structures:  
    3T19, 3T1A

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reverse Transcriptase
A, B
563HIV-1 M:B_HXB2RMutation(s): 1 
Gene Names: gag-polHIV-1 POL
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5MA
Query on 5MA

Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
5MA PDBBind:  3T1A Ki: 4.3 (nM) from 1 assay(s)
Binding MOAD:  3T1A Ki: 4.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.33α = 90
b = 154.23β = 90
c = 155.68γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2012-02-01
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-03-13
    Changes: Source and taxonomy