3I6O

Crystal structure of wild type HIV-1 protease with macrocyclic inhibitor GRL-0216A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, Protein-Ligand X-ray Structure, and Biological Evaluation of a Series of Novel Macrocyclic Human Immunodeficiency Virus-1 Protease Inhibitors to Combat Drug Resistance.

Ghosh, A.K.Kulkarni, S.Anderson, D.D.Hong, L.Baldridge, A.Wang, Y.F.Chumanevich, A.A.Kovalevsky, A.Y.Tojo, Y.Amano, M.Koh, Y.Tang, J.Weber, I.T.Mitsuya, H.

(2009) J.Med.Chem. 52: 7689-7705

  • DOI: 10.1021/jm900695w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic macrocyclic HIV protease inhibitors are described. The inhibitors are designed to effectively fill in the hydrophobic pocket in the S1'-S2' subsites and retai ...

    The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic macrocyclic HIV protease inhibitors are described. The inhibitors are designed to effectively fill in the hydrophobic pocket in the S1'-S2' subsites and retain all major hydrogen bonding interactions with the protein backbone similar to darunavir (1) or inhibitor 2. The ring size, the effect of methyl substitution, and unsaturation within the macrocyclic ring structure were assessed. In general, cyclic inhibitors were significantly more potent than their acyclic homologues, saturated rings were less active than their unsaturated analogues and a preference for 10- and 13-membered macrocylic rings was revealed. The addition of methyl substituents resulted in a reduction of potency. Both inhibitors 14b and 14c exhibited marked enzyme inhibitory and antiviral activity, and they exerted potent activity against multidrug-resistant HIV-1 variants. Protein-ligand X-ray structures of inhibitors 2 and 14c provided critical molecular insights into the ligand-binding site interactions.


    Organizational Affiliation

    Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GR6
Query on GR6

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Download CCD File 
B
(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(1S,2R)-1-benzyl-2-hydroxy-3-[(7E)-13-methoxy-1,1-dioxido-3,4,5,6,9,10-hexahydro-2H-11,1,2-benzoxathiazacyclotridecin-2-yl]propyl}carbamate
C32 H42 N2 O9 S
ZQJBDIZBNGQJDT-JZAADHNPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GR6EC50: 7 nM (100) BINDINGDB
GR6Ki: 0.1 nM (100) BINDINGDB
GR6IC50: 7 nM BINDINGMOAD
GR6Ki: 0.045 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.764α = 90.00
b = 86.328β = 90.00
c = 45.976γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
SHELXL-97refinement
MAR345data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description