1T7I

The structural and thermodynamic basis for the binding of TMC114, a next-generation HIV-1 protease inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor

Surleraux, D.L.N.G.Tahri, A.Verschueren, W.G.Pille, G.M.E.de Kock, H.A.Jonckers, T.H.M.Peeters, A.De Meyer, S.Azijn, H.Pauwels, R.de Bethune, M.-P.King, N.M.Prabu-Jeyabalan, M.Schiffer, C.A.Wigerinck, P.B.T.P.

(2005) J Med Chem 48: 1813-1822

  • DOI: 10.1021/jm049560p
  • Primary Citation of Related Structures:  
    1T3R, 1T7J, 1T7I

  • PubMed Abstract: 
  • The screening of known HIV-1 protease inhibitors against a panel of multi-drug-resistant viruses revealed the potent activity of TMC126 on drug-resistant mutants. In comparison to amprenavir, the improved affinity of TMC126 is largely the result of o ...

    The screening of known HIV-1 protease inhibitors against a panel of multi-drug-resistant viruses revealed the potent activity of TMC126 on drug-resistant mutants. In comparison to amprenavir, the improved affinity of TMC126 is largely the result of one extra hydrogen bond to the backbone of the protein in the P2 pocket. Modification of the substitution pattern on the phenylsulfonamide P2' substituent of TMC126 created an interesting SAR, with the close analogue TMC114 being found to have a similar antiviral activity against the mutant and the wild-type viruses. X-ray and thermodynamic studies on both wild-type and mutant enzymes showed an extremely high enthalpy driven affinity of TMC114 for HIV-1 protease. In vitro selection of mutants resistant to TMC114 starting from wild-type virus proved to be extremely difficult; this was not the case for other close analogues. Therefore, the extra H-bond to the backbone in the P2 pocket cannot be the only explanation for the interesting antiviral profile of TMC114. Absorption studies in animals indicated that TMC114 has pharmacokinetic properties comparable to currently approved HIV-1 protease inhibitors.


    Organizational Affiliation

    Tibotec BVBA, Generaal de Wittelaan L 11B 3, B-2800 Mechelen, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pol PolyproteinAB99Human immunodeficiency virus 1Mutation(s): 4 
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 P35963 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35963 
Go to UniProtKB:  P35963
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
017
Query on 017

Download CCD File 
A
(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
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
017Kd:  0.019999999552965164   nM  BindingDB
017IC50:  13   nM  BindingDB
017Ki:  2   nM  BindingDB
017IC50:  3.799999952316284   nM  BindingDB
017EC50:  13   nM  BindingDB
017EC50:  112   nM  BindingDB
017Ki:  0.019999999552965164   nM  BindingDB
017Ki:  0   nM  BindingDB
017Ki:  0.029999999329447746   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017Ki:  1.100000023841858   nM  BindingDB
017Ki:  0.2199999988079071   nM  BindingDB
017Ki:  0.3400000035762787   nM  BindingDB
017IC50:  0.05999999865889549   nM  BindingDB
017Ki:  0.009999999776482582   nM  BindingDB
017EC50:  0.25   nM  BindingDB
017Ki:  0.800000011920929   nM  BindingDB
017EC50:  1.600000023841858   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.858α = 90
b = 58.04β = 90
c = 61.656γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance