3FFI | pdb_00003ffi

HIV-1 RT with pyridone non-nucleoside inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3FFI/pdb

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


• Deposited: 2008-12-03 Released: 2009-12-15 
• Deposition Author(s): Harris, S.F., Villasenor, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Pyridone Diaryl Ether Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase

Kennedy-Smith, J., Sweeney, Z.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.69 kDa 
• Atom Count: 7,903 
• Modeled Residue Count: 952 
• Deposited Residue Count: 1,002 
• 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
RT p51	B	441	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
3OB	C [auth A]	3-chloro-5-({6-[2-(3,4-dihydroisoquinolin-2(1H)-yl)-2-oxoethyl]-3-(dimethylamino)-2-oxo-1,2-dihydropyridin-4-yl}oxy)benzonitrile C25 H23 Cl N4 O3 CLCCLHPVIUSCJF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.112	α = 90
b = 153.052	β = 90
c = 153.102	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Harris, S.F., Villasenor, A.

Revision History  

• Version 1.0: 2009-12-15
  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