6B3G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report



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

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

  • 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 sho ...

    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 .


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 ProteaseAB99Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag-pol
EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B (isolate BH5))
Explore P04587 
Go to UniProtKB:  P04587
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CKY
Query on CKY

Download CCD File 
B
N-(3-fluoro-2-{2-[(2S,6S)-6-methyl-1-(phenylsulfonyl)piperazin-2-yl]ethyl}phenyl)-3,3-bis(4-fluorophenyl)propanamide
C34 H34 F3 N3 O3 S
PKXSVHQEPFONSZ-FIPFOOKPSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.39α = 90
b = 85.83β = 90
c = 46.45γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release