6B3C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 inc ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 Protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04587
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CKS
Query on CKS

Download SDF File 
Download CCD File 
B
N-(3-fluoro-2-{2-[(2S,5R)-5-methyl-1-(phenylsulfonyl)piperazin-2-yl]ethyl}phenyl)-3,3-bis(4-fluorophenyl)propanamide
C34 H34 F3 N3 O3 S
WYXLVNGAPMCPRL-LXFBAYGMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.620α = 90.00
b = 86.060β = 90.00
c = 46.400γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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