3QLH

HIV-1 Reverse Transcriptase in Complex with Manicol at the RNase H Active Site and TMC278 (Rilpivirine) at the NNRTI Binding Pocket


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Synthesis, activity, and structural analysis of novel alpha-hydroxytropolone inhibitors of human immunodeficiency virus reverse transcriptase-associated ribonuclease H.

Chung, S.Himmel, D.M.Jiang, J.K.Wojtak, K.Bauman, J.D.Rausch, J.W.Wilson, J.A.Beutler, J.A.Thomas, C.J.Arnold, E.Le Grice, S.F.

(2011) J Med Chem 54: 4462-4473

  • DOI: 10.1021/jm2000757
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The α-hydroxytroplone, manicol (5,7-dihydroxy-2-isopropenyl-9-methyl-1,2,3,4-tetrahydro-benzocyclohepten-6-one), potently and specifically inhibits ribonuclease H (RNase H) activity of human immunodeficiency virus reverse transcriptase (HIV RT) in vi ...

    The α-hydroxytroplone, manicol (5,7-dihydroxy-2-isopropenyl-9-methyl-1,2,3,4-tetrahydro-benzocyclohepten-6-one), potently and specifically inhibits ribonuclease H (RNase H) activity of human immunodeficiency virus reverse transcriptase (HIV RT) in vitro. However, manicol was ineffective in reducing virus replication in culture. Ongoing efforts to improve the potency and specificity over the lead compound led us to synthesize 14 manicol derivatives that retain the divalent metal-chelating α-hydroxytropolone pharmacophore. These efforts were augmented by a high resolution structure of p66/p51 HIV-1 RT containing the nonnucleoside reverse transcriptase inhibitor (NNRTI), TMC278 and manicol in the DNA polymerase and RNase H active sites, respectively. We demonstrate here that several modified α-hydroxytropolones exhibit antiviral activity at noncytotoxic concentrations. Inclusion of RNase H active site mutants indicated that manicol analogues can occupy an additional site in or around the DNA polymerase catalytic center. Collectively, our studies will promote future structure-based design of improved α-hydroxytropolones to complement the NRTI and NNRTI currently in clinical use.


    Related Citations: 
    • Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
      Himmel, D.M., Maegley, K.A., Pauly, T.A., Bauman, J.D., Das, K., Dharia, C., Clark, A.D., Ryan, K., Hickey, M.J., Love, R.A., Hughes, S.H., Bergqvist, S., Arnold, E.
      (2009) Structure 17: 1625
    • 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
    • Sensitivity of Xenotropic Murine Leukemia Virus-Related Retrovirus Reverse Transcriptase-Associated Ribonuculease H to alpha-Hydroxytropolone Inhibitors
      Chung, S., Himmel, D.M., Jiang, J., Scarth, B., Wang, Y., Rausch, J.W., Lee, K., KewalRamani, V., Arnold, E., Gotte, M., Beutler, J.A., Thomas, C.R., Le Grice, S.F.J.
      () To be published --: --

    Organizational Affiliation

    RT Biochemistry Section, HIV Drug Resistance Program, National Cancer Institute-Frederick, Frederick, Maryland 21702, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase/ribonuclease H
A
555Human immunodeficiency virus type 1 BH10Mutation(s): 3 
Gene Names: gag-polPOL
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))
Go to UniProtKB:  P03366

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
reverse transcriptase/ribonuclease H
B
423Human immunodeficiency virus type 1 BH10Mutation(s): 1 
Gene Names: gag-polPOL
EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.4.23.16 (UniProt), 3.1.26.13 (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))
Go to UniProtKB:  P03366
Small Molecules
Ligands 5 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
MNK
Query on MNK

Download CCD File 
A
(2S)-5,7-dihydroxy-9-methyl-2-(prop-1-en-2-yl)-1,2,3,4-tetrahydro-6H-benzo[7]annulen-6-one
C15 H18 O3
XZCVMNQLRNHDOD-JTQLQIEISA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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: 2.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.926α = 90
b = 72.978β = 101.11
c = 108.377γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Non-polymer description
  • Version 1.2: 2013-02-27
    Changes: Database references
  • Version 1.3: 2015-06-17
    Changes: Non-polymer description
  • Version 1.4: 2018-01-24
    Changes: Database references