3TAM

Crystal structure of HIV-1 reverse transcriptase (K103N mutant) in complex with inhibitor M06


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and synthesis of pyridone inhibitors of non-nucleoside reverse transcriptase.

Gomez, R.Jolly, S.Williams, T.Tucker, T.Tynebor, R.Vacca, J.McGaughey, G.Lai, M.T.Felock, P.Munshi, V.DeStefano, D.Touch, S.Miller, M.Yan, Y.Sanchez, R.Liang, Y.Paton, B.Wan, B.L.Anthony, N.

(2011) Bioorg.Med.Chem.Lett. 21: 7344-7350

  • DOI: 10.1016/j.bmcl.2011.10.027

  • PubMed Abstract: 
  • Next generation NNRTIs are sought which possess both broad spectrum antiviral activity against key mutant strains and a high genetic barrier to the selection of new mutant viral strains. Pyridones were evaluated as an acyclic conformational constrain ...

    Next generation NNRTIs are sought which possess both broad spectrum antiviral activity against key mutant strains and a high genetic barrier to the selection of new mutant viral strains. Pyridones were evaluated as an acyclic conformational constraint to replace the aryl ether core of MK-4965 (1) and the more rigid indazole constraint of MK-6186 (2). The resulting pyridone compounds are potent inhibitors of HIV RT and have antiviral activity in cell culture that is superior to other next generation NNRTI's.


    Organizational Affiliation

    Department of West Point Discovery Chemistry, Merck Research Labs., 770 Sumneytown Pike, PO Box 4, West Point, PA 19486-0004, USA. Robert_gomez@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
563Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B
443Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M06
Query on M06

Download SDF File 
Download CCD File 
A
3-chloro-5-{[4-methyl-2-oxo-1-(2H-pyrazolo[3,4-b]pyridin-3-ylmethyl)-1,2-dihydropyridin-3-yl]oxy}benzonitrile
C20 H14 Cl N5 O2
YMRUCOCNLHJFRC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M06Ki: 3.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.910α = 90.00
b = 153.900β = 90.00
c = 155.690γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-08-04 
  • Released Date: 2011-10-26 
  • Deposition Author(s): Yan, Y.

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2012-01-18
    Type: Database references