2A4F

Synthesis and Activity of N-Axyl Azacyclic Urea HIV-1 Protease Inhibitors with High Potency Against Multiple Drug Resistant Viral Strains.

• PDB DOI: https://doi.org/10.2210/pdb2A4F/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-28 Released: 2005-09-20 
• Deposition Author(s): Zhao, C., Sham, H., Sun, M., Lin, S., Stoll, V., Stewart, K.D., Mo, H., Vasavanonda, S., Saldivar, A., McDonald, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.336 
• R-Value Work: 0.298 

Literature

Synthesis and activity of N-acyl azacyclic urea HIV-1 protease inhibitors with high potency against multiple drug resistant viral strains

Zhao, C., Sham, H.L., Sun, M., Stoll, V.S., Stewart, K.D., Lin, S., Mo, H., Vasavanonda, S., Saldivar, A., Park, C., McDonald, E.J., Marsh, K.C., Klein, L.L., Kempf, D.J., Norbeck, D.W.

(2005) Bioorg Med Chem Lett 15: 5499-5503

• PubMed: 16203141 
• DOI: https://doi.org/10.1016/j.bmcl.2005.08.093
• Primary Citation of Related Structures:  
  2A4F


• PubMed Abstract: 
  

  As part of our efforts to identify potent HIV-1 protease inhibitors that are active against resistant viral strains, structural modification of the azacyclic urea (I) was undertaken by incorporating acyl groups as P(1)' ligands. The extensive SAR study has yielded a series of N-acyl azacyclic ureas (II), which are highly potent against both wild-type and multiple PI-resistant viral strains.

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Organizational Affiliation: 

GPRD, Abbott Laboratories, Abbott Park, IL 60064-6123, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 22.25 kDa 
• Atom Count: 1,645 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: POL EC: 3.4.23.16
UniProt
Find proteins for Q9Q2G8 (Human immunodeficiency virus 1) Explore Q9Q2G8  Go to UniProtKB:  Q9Q2G8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAU	C [auth B]	(5R,6R)-5-BENZYL-6-HYDROXY-2,4-BIS(4-HYDROXY-3-METHOXYBENZYL)-1-[3-(4-HYDROXYPHENYL)PROPANOYL]-1,2,4-TRIAZEPAN-3-ONE C36 H39 N3 O8 LSKQYQOZDSRURR-QLWXXVCSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.336 
• R-Value Work: 0.298 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.008	α = 90
b = 85.742	β = 90
c = 46.646	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-20 
Deposition Author(s): Zhao, C., Sham, H., Sun, M., Lin, S., Stoll, V., Stewart, K.D., Mo, H., Vasavanonda, S., Saldivar, A., McDonald, E.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations