4G1Q

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with Rilpivirine (TMC278, Edurant), a non-nucleoside rt-inhibiting drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.

Kuroda, D.G.Bauman, J.D.Challa, J.R.Patel, D.Troxler, T.Das, K.Arnold, E.Hochstrasser, R.M.

(2013) Nat Chem 5: 174-181

  • DOI: 10.1038/nchem.1559

  • PubMed Abstract: 
  • The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render ...

    The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render the enzyme resistant. Here we report that water molecules play an essential role in this binding process. Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT. Two nitrile substituents, one on each arm of the drug, are used as vibrational probes of the structural dynamics within the binding pocket. Two-dimensional vibrational echo spectroscopy reveals that one nitrile group is unexpectedly hydrogen-bonded to a mobile water molecule, not identified in previous X-ray structures. Ultrafast nitrile-water dynamics are confirmed by simulations. A higher (1.51 Å) resolution X-ray structure also reveals a water-drug interaction network. Maintenance of a crucial anchoring hydrogen bond may help retain the potency of rilpivirine against pocket mutations despite the structural variations they cause.


    Related Citations: 
    • High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
      Das, K.,Bauman, J.D.,Clark, A.D.,Frenkel, Y.V.,Lewi, P.J.,Shatkin, A.J.,Hughes, S.H.,Arnold, E.
      (2008) Proc.Natl.Acad.Sci.USA 105: 1466
    • HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
      Das, K.,Martinez, S.E.,Bauman, J.D.,Arnold, E.
      (2012) Nat.Struct.Mol.Biol. 19: 253
    • Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
      Bauman, J.D.,Das, K.,Ho, W.C.,Baweja, M.,Himmel, D.M.,Clark, A.D.,Oren, D.A.,Boyer, P.L.,Hughes, S.H.,Shatkin, A.J.,Arnold, E.
      (2008) Nucleic Acids Res. 36: 5083
    • Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.
      Das, K.,Sarafianos, S.G.,Clark, A.D.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
      (2007) J.Mol.Biol. 365: 77
    • 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, 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.,Pauwels, R.,De Bethune, M.P.,Boyer, P.L.,Clark, P.,Hughes, S.H.,Janssen, P.A.,Arnold, E.
      (2004) J.Med.Chem. 47: 2550


    Organizational Affiliation

    Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Pennsylvania 19067, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase/ribonuclease H
A
557Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
p51 RT
B
428Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03366
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
T27
Query on T27

Download SDF File 
Download CCD File 
A
4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile
Rilpivirine
C22 H18 N6
YIBOMRUWOWDFLG-ONEGZZNKSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.713α = 90.00
b = 72.517β = 100.84
c = 109.514γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
ADSCdata collection
PHENIXrefinement
HKL-2000data scaling
PHENIXmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-06
    Type: Database references
  • Version 1.2: 2015-06-17
    Type: Non-polymer description