1SV5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


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:  
  • Also Cited By: 4G1Q, 5TXP, 5TXO, 5TXN, 5TXM, 5TXL, 3V81, 3V6D, 3V4I, 3QO9, 3BGR, 2ZE2, 2ZD1, 2IC3, 2IAJ

  • 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 patien ...

    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 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
    • 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.Mol.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


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse Transcriptase
A
560Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reverse Transcriptase
B
430Human immunodeficiency virus type 1 group M subtype BMutation(s): 2 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
65B
Query on 65B

Download SDF File 
Download CCD File 
A
4-({6-AMINO-5-BROMO-2-[(4-CYANOPHENYL)AMINO]PYRIMIDIN-4-YL}OXY)-3,5-DIMETHYLBENZONITRILE
Etravine; Etravirine
C20 H15 Br N6 O
PYGWGZALEOIKDF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
65BIC50: 370 nM (96) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.255 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 222.510α = 90.00
b = 67.740β = 107.47
c = 103.290γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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