2F80

HIV-1 Protease mutant D30N complexed with inhibitor TMC114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.149 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Effectiveness of Nonpeptide Clinical Inhibitor TMC-114 on HIV-1 Protease with Highly Drug Resistant Mutations D30N, I50V, and L90M.

Kovalevsky, A.Y.Tie, Y.Liu, F.Boross, P.I.Wang, Y.F.Leshchenko, S.Ghosh, A.K.Harrison, R.W.Weber, I.T.

(2006) J Med Chem 49: 1379-1387

  • DOI: 10.1021/jm050943c
  • Primary Citation of Related Structures:  
    2F81, 2F80, 2F8G

  • PubMed Abstract: 
  • The potent new antiviral inhibitor TMC-114 (UIC-94017) of HIV-1 protease (PR) has been studied with three PR variants containing single mutations D30N, I50V, and L90M, which provide resistance to the major clinical inhibitors. The inhibition constant ...

    The potent new antiviral inhibitor TMC-114 (UIC-94017) of HIV-1 protease (PR) has been studied with three PR variants containing single mutations D30N, I50V, and L90M, which provide resistance to the major clinical inhibitors. The inhibition constants (K(i)) of TMC-114 for mutants PR(D30N), PR(I50V), and PR(L90M) were 30-, 9-, and 0.14-fold, respectively, relative to wild-type PR. The molecular basis for the inhibition was analyzed using high-resolution (1.22-1.45 A) crystal structures of PR mutant complexes with TMC-114. In PR(D30N), the inhibitor has a water-mediated interaction with the side chain of Asn30 rather than the direct interaction observed in PR, which is consistent with the relative inhibition. Similarly, in PR(I50V) the inhibitor loses favorable hydrophobic interactions with the side chain of Val50. TMC-114 has additional van der Waals contacts in PR(L90M) structure compared to the PR structure, leading to a tighter binding of the inhibitor. The observed changes in PR structure and activity are discussed in relation to the potential for development of resistant mutants on exposure to TMC-114.


    Organizational Affiliation

    Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POL POLYPROTEINAB99Human immunodeficiency virus 1Mutation(s): 6 
Gene Names: 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download CCD File 
B
(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE
C27 H37 N3 O7 S
CJBJHOAVZSMMDJ-HEXNFIEUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
017Ki:  0.2199999988079071   nM  BindingDB
017IC50:  3.799999952316284   nM  BindingDB
017Ki:  0.3400000035762787   nM  BindingDB
017Ki:  2   nM  BindingDB
017Kd:  0.019999999552965164   nM  BindingDB
017Ki:  0.019999999552965164   nM  BindingDB
017EC50:  1.600000023841858   nM  BindingDB
017EC50:  112   nM  BindingDB
017IC50:  13   nM  BindingDB
017Ki:  6.599999904632568   nM  Binding MOAD
017Ki:  0.800000011920929   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017Ki:  0.029999999329447746   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
017EC50:  0.25   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
17Ki :  6.599999904632568   nM  PDBBind
017IC50:  0.05999999865889549   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017EC50:  13   nM  BindingDB
017Ki:  0   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.492α = 90
b = 86.134β = 90
c = 45.943γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description