4FE6

Crystal Structure of HIV-1 Protease in Complex with an enamino-oxindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4FE6/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 (BRU ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-29 Released: 2012-07-18 
• Deposition Author(s): Silva, A.M., Eissenstat, M., Guerassina, T., Gulnik, S., Afonina, E., Yu, B., Erickson, J., Ludke, D., Yokoe, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Enamino-oxindole HIV protease inhibitors.

Eissenstat, M., Guerassina, T., Gulnik, S., Afonina, E., Silva, A.M., Ludtke, D., Yokoe, H., Yu, B., Erickson, J.

(2012) Bioorg Med Chem Lett 22: 5078-5083

• PubMed: 22749283 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.120
• Primary Citation of Related Structures:  
  4FE6


• PubMed Abstract: 
  

  We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2' subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiviral IC(50) in the low nM range against WT HIV and against a panel of multi-drug resistant (MDR) strains.

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Organizational Affiliation: 

Sequoia Pharmaceuticals, Inc., Gaithersburg, MD 10878, 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: 11.45 kDa 
• Atom Count: 896 
• Modelled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV protease	A	99	Human immunodeficiency virus type 1 (BRU ISOLATE)	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0TQ	B [auth A]	(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[({(3Z)-3-[1-(methylamino)ethylidene]-2-oxo-2,3-dihydro-1H-indol-5-yl}sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate C32 H42 N4 O8 S CJXWCYBPIXFWOP-PEXZKGFOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.654	α = 90
b = 62.654	β = 90
c = 82.361	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-18 
Deposition Author(s): Silva, A.M., Eissenstat, M., Guerassina, T., Gulnik, S., Afonina, E., Yu, B., Erickson, J., Ludke, D., Yokoe, H.

Revision History  

• Version 1.0: 2012-07-18
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations