3DI6 | pdb_00003di6

HIV-1 RT with pyridazinone non-nucleoside inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3DI6/pdb

• Classification: TRANSFERASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-19 Released: 2008-08-19 
• Deposition Author(s): Harris, S.F., Villasenor, A., Dunten, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.222 (DCC) 

Literature

Discovery and optimization of pyridazinone non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Sweeney, Z.K., Dunn, J.P., Li, Y., Heilek, G., Dunten, P., Elworthy, T.R., Han, X., Harris, S.F., Hirschfeld, D.R., Hogg, J.H., Huber, W., Kaiser, A.C., Kertesz, D.J., Kim, W., Mirzadegan, T., Roepel, M.G., Saito, Y.D., Silva, T.M., Swallow, S., Tracy, J.L., Villasenor, A., Vora, H., Zhou, A.S., Klumpp, K.

(2008) Bioorg Med Chem Lett 18: 4352-4354

• PubMed: 18632268 
• DOI: https://doi.org/10.1016/j.bmcl.2008.06.072
• Primary Citation Related Structures: 
  3DI6


• PubMed Abstract: 
  

  A series of benzyl pyridazinones were evaluated as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). Several members of this series showed good activity against the wild-type virus and NNRTI-resistant viruses. The binding of inhibitor 5a to HIV-RT was analyzed by surface plasmon resonance spectroscopy. Pharmacokinetic studies of 5a in rat and dog demonstrated that this compound has good oral bioavailability in animal species. The crystal structure of a complex between HIV-RT and inhibitor 4c is also described.

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Organizational Affiliation: 
• Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.44 kDa 
• Atom Count: 7,908 
• Modeled Residue Count: 951 
• Deposited Residue Count: 1,001 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reverse transcriptase/ribonuclease H	A	561	HIV-1 M:B_HXB2R	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
p51 RT	B	440	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDZ	C [auth A]	6-(4-chloro-2-fluoro-3-phenoxybenzyl)pyridazin-3(2H)-one C17 H12 Cl F N2 O2 NOVPOXGMADEKPP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.222 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.046	α = 90
b = 153.51	β = 90
c = 154.551	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Harris, S.F., Villasenor, A., Dunten, P.

Revision History  

• Version 1.0: 2008-08-19
  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