2BE2

Crystal structure of HIV-1 reverse transcriptase (RT) in complex with R221239


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains.

Himmel, D.M.Das, K.Clark Jr., A.D.Hughes, S.H.Benjahad, A.Oumouch, S.Guillemont, J.Coupa, S.Poncelet, A.Csoka, I.Meyer, C.Andries, K.Nguyen, C.H.Grierson, D.S.Arnold, E.

(2005) J Med Chem 48: 7582-7591

  • DOI: 10.1021/jm0500323
  • Primary Citation of Related Structures:  
    2B5J, 2BAN, 2BE2

  • PubMed Abstract: 
  • In the treatment of AIDS, the efficacy of all drugs, including non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), has been limited by the rapid appearance of drug-resistant viruses. Lys103Asn, Tyr181Cys, and Tyr188Leu are some of the most common RT mutations that cause resistance to NNRTIs in the clinic ...

    In the treatment of AIDS, the efficacy of all drugs, including non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT), has been limited by the rapid appearance of drug-resistant viruses. Lys103Asn, Tyr181Cys, and Tyr188Leu are some of the most common RT mutations that cause resistance to NNRTIs in the clinic. We report X-ray crystal structures for RT complexed with three different pyridinone derivatives, R157208, R165481, and R221239, at 2.95, 2.9, and 2.43 A resolution, respectively. All three ligands exhibit nanomolar or subnanomolar inhibitory activity against wild-type RT, but varying activities against drug-resistant mutants. R165481 and R221239 differ from most NNRTIs in that binding does not involve significant contacts with Tyr181. These compounds strongly inhibit wild-type HIV-1 RT and drug-resistant variants, including Tyr181Cys and Lys103Asn RT. These properties result in part from an iodine atom on the pyridinone ring of both inhibitors that interacts with the main-chain carbonyl oxygen of Tyr188. An acrylonitrile substituent on R165481 substantially improves the activity of the compound against wild-type RT (and several mutants) and provides a way to generate novel inhibitors that could interact with conserved elements of HIV-1 RT at the polymerase catalytic site. In R221239, there is a flexible linker to a furan ring that permits interactions with Val106, Phe227, and Pro236. These contacts appear to enhance the inhibitory activity of R221239 against the HIV-1 strains that carry the Val106Ala, Tyr188Leu, and Phe227Cys mutations.


    Related Citations: 
    • 3-iodo-4-phenoxypyridinones (IOPY's), a New Family of Highly Potent Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase
      Benjahad, A., Guillemont, J., Andries, K., Nguyen, C.H., Grierson, D.S.
      (2003) Bioorg Med Chem Lett 13: 4309
    • 4-Benzyl and 4-Benzoyl-3-Dimethylaminopyridin-2(1H)-Ones: In Vitro Evaluation of New C-3-Amino-Substituted and C-5,6-Alkyl-Substituted Analogues Against Clinically Important HIV Mutant Strains
      Benjahad, A., Croisy, M., Monneret, C., Bisagni, E., Mabire, D., Coupa, S., Poncelet, A., Csoka, I., Guillemont, J., Meyer, C., Andries, K., Pauwels, R., De Bethune, M.P., Himmel, D.M., Das, K., Arnold, E., Nguyen, C.H., Grierson, D.S.
      (2005) J Med Chem 48: 1948
    • 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.H., 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.J., Arnold, E.
      (2004) J Med Chem 47: 2550
    • 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
    • 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.J., Hughes, S.H., Arnold, E.
      (1995) Nat Struct Biol 2: 407

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
REVERSE TRANSCRIPTASE P66 SUBUNITA560Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
REVERSE TRANSCRIPTASE P51 SUBUNITB430Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: POL
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03366
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseC, D 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R22
Query on R22

Download Ideal Coordinates CCD File 
H [auth A]4-(3,5-DIMETHYLPHENOXY)-5-(FURAN-2-YLMETHYLSULFANYLMETHYL)-3-IODO-6-METHYLPYRIDIN-2(1H)-ONE
C20 H20 I N O3 S
YZLKVEDFWLGNQP-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
G [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
R22 PDBBind:  2BE2 IC50: 2 (nM) from 1 assay(s)
Binding MOAD:  2BE2 IC50: 2 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
C, DsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.853α = 90
b = 68.798β = 107.22
c = 104.43γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary