1SV5

CRYSTAL STRUCTURE OF K103N MUTANT HIV-1 REVERSE TRANSCRIPTASE (RT) IN COMPLEX WITH JANSSEN-R165335


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 Variants

Das, K.Clark Jr., A.D.Lewi, P.J.Heeres, J.De Jonge, M.R.Koymans, L.M.Vinkers, H.M.Daeyaert, F.Ludovici, D.W.Kukla, M.J.De Corte, B.Kavash, R.W.Ho, C.Y.Ye, H.Lichtenstein, M.A.Andries, K.Pauwles, R.Debethune, M.-P.Boyer, P.L.Clark, P.Hughes, S.H.Janssen, P.A.Arnold, E.

(2004) J Med Chem 47: 2550-2560

  • DOI: 10.1021/jm030558s
  • Primary Citation of Related Structures:  
    1S6Q, 1S6P, 1S9G, 1S9E, 1SUQ, 1SV5

  • PubMed Abstract: 
  • Anti-AIDS drug candidate and non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC125-R165335 (etravirine) caused an initial drop in viral load similar to that observed with a five-drug combination in naïve patients and retains potency in patients infected with NNRTI-resistant HIV-1 variants ...

    Anti-AIDS drug candidate and non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC125-R165335 (etravirine) caused an initial drop in viral load similar to that observed with a five-drug combination in naïve patients and retains potency in patients infected with NNRTI-resistant HIV-1 variants. TMC125-R165335 and related anti-AIDS drug candidates can bind the enzyme RT in multiple conformations and thereby escape the effects of drug-resistance mutations. Structural studies showed that this inhibitor and other diarylpyrimidine (DAPY) analogues can adapt to changes in the NNRTI-binding pocket in several ways: (1). DAPY analogues can bind in at least two conformationally distinct modes; (2). within a given binding mode, torsional flexibility ("wiggling") of DAPY analogues permits access to numerous conformational variants; and (3). the compact design of the DAPY analogues permits significant repositioning and reorientation (translation and rotation) within the pocket ("jiggling"). Such adaptations appear to be critical for potency against wild-type and a wide range of drug-resistant mutant HIV-1 RTs. Exploitation of favorable components of inhibitor conformational flexibility (such as torsional flexibility about strategically located chemical bonds) can be a powerful drug design concept, especially for designing drugs that will be effective against rapidly mutating targets.


    Related Citations: 
    • Structure of HIV-1 RT/TIBO R 86183 Complex Reveals Similarity in the Binding of Diverse Nonnucleoside Inhibitors
      Ding, J., Das, K., Moereels, H., Koymans, L., Andries, K., Janssen, P.A., Hughes, S.H., Arnold, E.
      (1995) Nat Struct Biol 2: 407
    • Structure of HIV-1 Reverse Transcriptase in a Complex with the Non-Nucleoside Inhibitor Alpha-Apa R 95845 at 2.8 A Resolution
      Ding, J., Das, K., Tantillo, C., Zhang, W., Clark Jr., A.D., Jessen, S., Lu, X., Hsiou, Y., Jacobo-Molina, A., Andries, K., Pauwels, R., Moereels, H., Koymans, L., Janssen, P.A.J., Smith Jr., R.H., Kroeger Koepke, M., Michejda, C.J., Hughes, S.H., Arnold, E.
      (1995) Structure 3: 365
    • Crystal Structures of 8-Cl and 9-Cl TIBO Complexed with Wild-Type HIV-1 RT and 8-Cl TIBO Complexed with the Tyr181Cys HIV-1 RT Drug-Resistant Mutant
      Das, K., Ding, J., Hsiou, Y., Clark Jr., A.D., Moereels, H., Koymans, L., Andries, K., Pauwels, R., Janssen, P.A., Boyer, P.L., Clark, P., Smith Jr., R.H., Kroeger Smith, M.B., Michejda, C.J., Hughes, S.H., Arnold, E.
      (1996) J Mol Biol 264: 1085
    • Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA Template-Primer and an Antibody Fab Fragment at 2.8 A Resolution
      Ding, J., Das, K., Hsiou, Y., Sarafianos, S.G., Clark Jr., A.D., Jacobo-Molina, A., Tantillo, C., Hughes, S.H., Arnold, E.
      (1998) J Mol Biol 284: 1095
    • Evolution of Anti-HIV Drug Candidates. Part 3: Diarylpyrimidine (Dapy) Analogues
      Ludovici, D.W., De Corte, B.L., Kukla, M.J., Ye, H., Ho, C.Y., Lichtenstein, M.A., Kavash, R.W., Andries, K., De Bethune, M.P., Azijn, H., Pauwels, R., Lewi, P.J., Heeres, J., Koymans, L.M., De Jonge, M.R., Van Aken, K.J., Daeyaert, F.F., Das, K., Arnold, E., Janssen, P.A.
      (2001) Bioorg Med Chem Lett 11: 2235

    Organizational Affiliation

    Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse TranscriptaseA560Human immunodeficiency virus 1Mutation(s): 2 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse TranscriptaseB430Human immunodeficiency virus 1Mutation(s): 2 
EC: 2.7.7.49 (PDB Primary Data), 3.4.23.16 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03366 
Go to UniProtKB:  P03366
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
65B (Subject of Investigation/LOI)
Query on 65B

Download Ideal Coordinates CCD File 
C [auth A]4-({6-AMINO-5-BROMO-2-[(4-CYANOPHENYL)AMINO]PYRIMIDIN-4-YL}OXY)-3,5-DIMETHYLBENZONITRILE
C20 H15 Br N6 O
PYGWGZALEOIKDF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
65B BindingDB:  1SV5 IC50: 370 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.51α = 90
b = 67.74β = 107.47
c = 103.29γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2004-03-27 
  • Released Date: 2004-05-11 
  • Deposition Author(s): Das, K., Arnold, E.

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-18
    Changes: Non-polymer description