3E01 | pdb_00003e01

HIV-RT with non-nucleoside inhibitor annulated pyrazole 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.279 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.237 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3E01

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm800527x
  • Primary Citation Related Structures: 
    3DYA, 3E01

  • 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-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

Macromolecule Content 

  • Total Structure Weight: 116.53 kDa 
  • Atom Count: 7,840 
  • Modeled Residue Count: 953 
  • Deposited Residue Count: 1,001 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein561HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Gag-Pol polyprotein440HIV-1 M:B_HXB2RMutation(s): 0 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (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
PZ2

Query on PZ2



Download:Ideal Coordinates CCD File
C [auth A]3-[2-bromo-4-(1H-pyrazolo[3,4-c]pyridazin-3-ylmethyl)phenoxy]-5-methylbenzonitrile
C20 H14 Br N5 O
YYGZQXRLQMFHDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.279 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.237 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.897α = 90
b = 152.277β = 90
c = 153.987γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations