3DYA

HIV-1 RT with non-nucleoside inhibitor annulated Pyrazole 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design of annulated pyrazoles as inhibitors of HIV-1 reverse transcriptase

Sweeney, Z.K.Harris, S.F.Arora, S.F.Javanbakht, H.Li, Y.Fretland, J.Davidson, J.P.Billedeau, J.R.Gleason, S.K.Hirschfeld, D.Kennedy-Smith, J.J.Mirzadegan, T.Roetz, R.Smith, M.Sperry, S.Suh, J.M.Wu, J.Tsing, S.Villasenor, A.G.Paul, A.Su, G.Heilek, G.Hang, J.Q.Zhou, A.S.Jernelius, J.A.Zhang, F.J.Klumpp, K.

(2008) J.Med.Chem. 51: 7449-7458

  • DOI: 10.1021/jm800527x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are recommended components of preferred combination antiretroviral therapies used for the treatment of HIV. These regimens are extremely effective in suppressing virus replication. Structure-ba ...

    Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are recommended components of preferred combination antiretroviral therapies used for the treatment of HIV. These regimens are extremely effective in suppressing virus replication. Structure-based optimization of diaryl ether inhibitors led to the discovery of a new series of pyrazolo[3,4-c]pyridazine NNRTIs that bind the reverse transcriptase enzyme of human immunodeficiency virus-1 (HIV-RT) in an expanded volume relative to most other inhibitors in this class.The binding mode maintains the beta13 and beta14 strands bearing Pro236 in a position similar to that in the unliganded reverse transcriptase structure, and the distribution of interactions creates the opportunity for substantial resilience to single point mutations. Several pyrazolopyridazine NNRTIs were found to be highly effective against wild-type and NNRTI-resistant viral strains in cell culture.


    Organizational Affiliation

    Department of Medicinal Chemistry, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA. zachary.sweeney@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
REVERSE TRANSCRIPTASE/RIBONUCLEASE H
A
561Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
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
440Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
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
PZL
Query on PZL

Download SDF File 
Download CCD File 
A
3-[6-bromo-2-fluoro-3-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-chlorobenzonitrile
C19 H10 Br Cl F N5 O
OHQMEDBYNUAVNE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PZLIC50: 3 nM (99) BINDINGDB
PZLEC50: 1 - 4 nM (100) BINDINGDB
PZLIC50: 3 nM BINDINGMOAD
PZLIC50: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 117.662α = 90.00
b = 153.669β = 90.00
c = 155.795γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance