3TH9 | pdb_00003th9

Crystal Structure of HIV-1 Protease Mutant Q7K V32I L63I with a cyclic sulfonamide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3TH9/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus type 1 lw12.3 isolate
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-08-18 Released: 2011-09-28 
• Deposition Author(s): Orth, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.190 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.181 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Design, Synthesis, and X-ray Crystallographic Analysis of a Novel Class of HIV-1 Protease Inhibitors.

Ganguly, A.K., Alluri, S.S., Caroccia, D., Biswas, D., Wang, C.H., Kang, E., Zhang, Y., McPhail, A.T., Carroll, S.S., Burlein, C., Munshi, V., Orth, P., Strickland, C.

(2011) J Med Chem 54: 7176-7183

• PubMed: 21916489 
• DOI: https://doi.org/10.1021/jm200778q
• Primary Citation Related Structures: 
  3TH9


• PubMed Abstract: 
  

  In the present paper, design, synthesis, X-ray crystallographic analysis, and HIV-1 protease inhibitory activities of a novel class of compounds are disclosed. Compounds 28-30, 32, 35, and 40 were synthesized and found to be inhibitors of the HIV-1 protease. The crucial step in their synthesis involved an unusual endo radical cyclization process. Absolute stereochemistry of the three asymmetric centers in the above compounds have been established to be (4S,2'R,3'S) for optimal potency. X-ray crystallographic analysis has been used to determine the binding mode of the inhibitors to the HIV-1 protease.

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Organizational Affiliation: 
• Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey 07030, United States. [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: 22.59 kDa 
• Atom Count: 1,813 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, B	99	Human immunodeficiency virus type 1 lw12.3 isolate	Mutation(s): 3  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P0C6F2 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123)) Explore P0C6F2  Go to UniProtKB:  P0C6F2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9Y9	C [auth A], D [auth B]	tert-butyl {(2S,3R)-4-[(4S)-7-fluoro-4-methyl-1,1-dioxido-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}carbamate C25 H33 F N2 O5 S KMJVCYPPUACVBA-BULFRSBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.190 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.181 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.68	α = 90
b = 85.89	β = 90
c = 46.27	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SCALA	data scaling
AMoRE	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Orth, P.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations