3I8W

Crystal structure of a metallacarborane inhibitor bound to HIV protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design of HIV Protease Inhibitors Based on Inorganic Polyhedral Metallacarboranes

Pokorna, J.Brynda, J.Cigler, P.Fanfrlik, J.Sieglova, I.Oberwinkler, H.Hobza, P.Kral, V.Konvalinka, J.

(2009) J.Med.Chem. 52: 7132-7141

  • DOI: 10.1021/jm9011388

  • PubMed Abstract: 
  • HIV protease (HIV PR) is a primary target for anti-HIV drug design. We have previously identified and characterized substituted metallacarboranes as a new class of HIV protease inhibitors. In a structure-guided drug design effort, we connected the tw ...

    HIV protease (HIV PR) is a primary target for anti-HIV drug design. We have previously identified and characterized substituted metallacarboranes as a new class of HIV protease inhibitors. In a structure-guided drug design effort, we connected the two cobalt bis(dicarbollide) clusters with a linker to substituted ammonium group and obtained a set of compounds based on a lead formula [H(2)N-(8-(C(2)H(4)O)(2)-1,2-C(2)B(9)H(10))(1',2'-C(2)B(9)H(11))-3,3'-Co)(2)]Na. We explored inhibition properties of these compounds with various substitutions, determined the HIV PR:inhibitor crystal structure, and computationally explored the conformational space of the linker. Our results prove the capacity of linker-substituted dual-cage cobalt bis(dicarbollides) as lead compounds for design of more potent inhibitors of HIV PR.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 16610 Praha 6, Czech Republic. rezacova@uochb.cas.cz




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A
99Human immunodeficiency virus type 1 group M subtype BMutation(s): 3 
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
CB5
Query on CB5

Download SDF File 
Download CCD File 
A
COBALT BIS(1,2-DICARBOLLIDE)
C4 H22 B18 Co
LCYCHKJZRWLTHW-NQCAZLHCSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CB5Ki: 4.9 nM BINDINGMOAD
CB5Ki: 4.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.158α = 90.00
b = 92.343β = 90.00
c = 48.952γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data collection
MOLREPphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-07-10 
  • Released Date: 2009-12-01 
  • Deposition Author(s): Rezacova, P.

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance