6B38

Crystal Structure of HIV Protease complexed with N-(3-fluoro-2-(2-((2S,6R)-6-methyl-1-(phenylsulfonyl)piperazin-2-yl)ethyl)phenyl)-3,3-bis(4-fluorophenyl)propanamide

• PDB DOI: https://doi.org/10.2210/pdb6B38/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Human immunodeficiency virus 1
• Mutation(s): No 


• Deposited: 2017-09-21 Released: 2018-01-03 
• Deposition Author(s): Su, H.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Design and Synthesis of Piperazine Sulfonamide Cores Leading to Highly Potent HIV-1 Protease Inhibitors.

Bungard, C.J., Williams, P.D., Schulz, J., Wiscount, C.M., Holloway, M.K., Loughran, H.M., Manikowski, J.J., Su, H.P., Bennett, D.J., Chang, L., Chu, X.J., Crespo, A., Dwyer, M.P., Keertikar, K., Morriello, G.J., Stamford, A.W., Waddell, S.T., Zhong, B., Hu, B., Ji, T., Diamond, T.L., Bahnck-Teets, C., Carroll, S.S., Fay, J.F., Min, X., Morris, W., Ballard, J.E., Miller, M.D., McCauley, J.A.

(2017) ACS Med Chem Lett 8: 1292-1297

• PubMed: 29259750 
• DOI: https://doi.org/10.1021/acsmedchemlett.7b00386
• Primary Citation of Related Structures:  
  6B36, 6B38, 6B3C, 6B3F, 6B3G, 6B3H


• PubMed Abstract: 
  

  Using the HIV-1 protease binding mode of MK-8718 and PL-100 as inspiration, a novel aspartate binding bicyclic piperazine sulfonamide core was designed and synthesized. The resulting HIV-1 protease inhibitor containing this core showed an 60-fold increase in enzyme binding affinity and a 10-fold increase in antiviral activity relative to MK-8718 .

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Organizational Affiliation: 

Merck & Co., Inc., 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.96 kDa 
• Atom Count: 1,772 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5)) Explore P04587  Go to UniProtKB:  P04587

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CKM	D [auth B], E [auth B]	N-(3-fluoro-2-{2-[(2S,6R)-6-methyl-1-(phenylsulfonyl)piperazin-2-yl]ethyl}phenyl)-3,3-bis(4-fluorophenyl)propanamide C34 H34 F3 N3 O3 S PKXSVHQEPFONSZ-LXFBAYGMSA-N
CL	C [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.33	α = 90
b = 85.78	β = 90
c = 46.55	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-03 
Deposition Author(s): Su, H.P.

Revision History  

• Version 1.0: 2018-01-03
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references