4DFG

Crystal Structure of Wild-type HIV-1 Protease with Cyclopentyltetrahydro- furanyl Urethanes as P2-ligand, GRL-0249A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Substituent effects on P2-cyclopentyltetrahydrofuranyl urethanes: Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors.

Ghosh, A.K.Chapsal, B.D.Steffey, M.Agniswamy, J.Wang, Y.F.Amano, M.Weber, I.T.Mitsuya, H.

(2012) Bioorg.Med.Chem.Lett. 22: 2308-2311

  • DOI: 10.1016/j.bmcl.2012.01.061

  • PubMed Abstract: 
  • The design, synthesis, and biological evaluation of novel C3-substituted cyclopentyltetrahydrofuranyl (Cp-THF)-derived HIV-1 protease inhibitors are described. Various C3-functional groups on the Cp-THF ligand were investigated in order to maximize t ...

    The design, synthesis, and biological evaluation of novel C3-substituted cyclopentyltetrahydrofuranyl (Cp-THF)-derived HIV-1 protease inhibitors are described. Various C3-functional groups on the Cp-THF ligand were investigated in order to maximize the ligand-binding site interactions in the flap region of the protease. Inhibitors 3c and 3d have displayed the most potent enzyme inhibitory and antiviral activity. Both inhibitors have maintained impressive activity against a panel of multidrug resistant HIV-1 variants. A high-resolution X-ray crystal structure of 3c-bound HIV-1 protease revealed a number of important molecular insights into the ligand-binding site interactions.


    Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. akghosh@purdue.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 5 
Gene Names: gag-pol
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03367
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
0JV
Query on 0JV

Download SDF File 
Download CCD File 
B
methyl N-[(3S,3aR,5R,6aR)-5-[[(2S,3R)-4-[(4-methoxyphenyl)sulfonyl-(2-methylpropyl)amino]-3-oxidanyl-1-phenyl-butan-2-yl]carbamoyloxy]-3,3a,4,5,6,6a-hexahydro-2H-cyclopenta[b]furan-3-yl]carbamate
C31 H43 N3 O9 S
XXQYXAWGNBWMGJ-YZGPKJBYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0JVKi: 0.0018 nM BINDINGMOAD
0JVKi: 0.0018 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.580α = 90.00
b = 85.930β = 90.00
c = 45.990γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release