1YT9

HIV Protease with oximinoarylsulfonamide bound

• PDB DOI: https://doi.org/10.2210/pdb1YT9/pdb

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


• Deposited: 2005-02-10 Released: 2005-04-12 
• Deposition Author(s): Yeung, C.M., Klein, L.L., Flentge, C.A., Randolph, J.T., Zhao, C., Sun, M., Dekhtyar, T., Stoll, V.S., Kempf, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.338 (Depositor) 
• R-Value Work: 
  0.248 (Depositor) 

Literature

Oximinoarylsulfonamides as potent HIV protease inhibitors.

Yeung, C.M., Klein, L.L., Flentge, C.A., Randolph, J.T., Zhao, C., Sun, M., Dekhtyar, T., Stoll, V.S., Kempf, D.J.

(2005) Bioorg Med Chem Lett 15: 2275-2278

• PubMed: 15837308 
• DOI: https://doi.org/10.1016/j.bmcl.2005.03.008
• Primary Citation of Related Structures:  
  1YT9


• PubMed Abstract: 
  

  The need for a potent HIV protease inhibitor (PI) to combat emerging PI-resistant viruses is anticipated. Analogs formulated from the combination of structural fragments of Ritonavir, Lopinavir, and Amprenavir were synthesized. Analogs containing the oxime pharmacophore were found to have improved activities against both wild type and resistant (A17) viruses. The synthesis and structure-activity relationships (SAR) based upon the in vitro IC50 of this series of compounds are reported.

---

Organizational Affiliation: 

Abbott Laboratories, GPRD, D-47D, Building AP52N, 200 Abbott Park Road, Abbott Park, IL 60064-3501, 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: 22.31 kDa 
• Atom Count: 1,564 
• 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
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OIS	C [auth A]	(S)-N-((2S,3R)-3-HYDROXY-4-(4-((E)-(HYDROXYIMINO)METHYL)-N-ISOBUTYLPHENYLSULFONAMIDO)-1-PHENYLBUTAN-2-YL)-3-METHYL-2-(3 -((2-METHYLTHIAZOL-4-YL)METHYL)-2-OXOIMIDAZOLIDIN-1-YL)BUTANAMIDE C34 H46 N6 O6 S2 PJLSJXTZOMOVBI-KKWNBLJUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OIS	BindingDB:  1YT9	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.338 (Depositor) 
• R-Value Work:  0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.041	α = 90
b = 85.954	β = 90
c = 46.033	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Yeung, C.M., Klein, L.L., Flentge, C.A., Randolph, J.T., Zhao, C., Sun, M., Dekhtyar, T., Stoll, V.S., Kempf, D.J.

Revision History  

• Version 1.0: 2005-04-12
  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, Structure summary