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 
  • R-Value Observed: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    4G1Q

  • 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 U S A 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse transcriptase/ribonuclease HA557Human immunodeficiency virus type 1 BH10Mutation(s): 3 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (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
p51 RTB428Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-pol
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.13 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T27
Query on T27

Download CCD File 
A
4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile
C22 H18 N6
YIBOMRUWOWDFLG-ONEGZZNKSA-N
 Ligand Interaction
SO4
Query on SO4

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

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

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T27IC50:  68   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.713α = 90
b = 72.517β = 100.84
c = 109.514γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references
  • Version 1.2: 2015-06-17
    Changes: Non-polymer description
  • Version 1.3: 2018-01-24
    Changes: Structure summary