1C1C

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH TNK-6123


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of MKC-442 (emivirine) analogues with improved activity against drug-resistant HIV mutants.

Hopkins, A.L.Ren, J.Tanaka, H.Baba, M.Okamato, M.Stuart, D.I.Stammers, D.K.

(1999) J Med Chem 42: 4500-4505

  • DOI: 10.1021/jm990192c
  • Primary Citation of Related Structures:  
    1C1C, 1C1B

  • PubMed Abstract: 
  • Two analogues of the nonnucleoside inhibitor of HIV-1 RT, MKC-442 (emivirine), containing different C6 substituents have been designed to be less susceptible to the commonly found drug-resistance mutation of Tyr181Cys. Compound TNK-6123 had a C6 thiocycl ...

    Two analogues of the nonnucleoside inhibitor of HIV-1 RT, MKC-442 (emivirine), containing different C6 substituents have been designed to be less susceptible to the commonly found drug-resistance mutation of Tyr181Cys. Compound TNK-6123 had a C6 thiocyclohexyl group designed to have more flexibility in adapting to the mutated drug-binding site. GCA-186 had additional 3',5'-dimethyl substituents aimed at forming close contacts with the conserved residue Trp229. Both compounds showed approximately 30-fold greater inhibitory effect than MKC-442 to the Tyr181Cys mutant virus as well as to the clinically important Lys103Asn virus. X-ray crystallographic structure determination of complexes with HIV-1 RT confirmed the predicted binding modes. These strategies might be used to improve the resilience of other NNRTI series against common drug-resistance mutations.


    Related Citations: 
    • Crystallographic Analysis of the Binding Modes of Thiazoloisoindolinone non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase and Comparison with Modelling Studies
      Ren, J., Esnouf, R.M., Hopkins, A.L., Stuart, D.I., Stammers, D.K.
      (1999) J Med Chem 42: 3845
    • Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives
      Ren, J., Esnouf, R.M., Hopkins, A.L., Warren, J., Balzarini, J., Stuart, D.I.
      (1998) Biochemistry 37: 14394
    • 3'-azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes
      Ren, J., Esnouf, R.M., Hopkins, A.L., Jones, E.Y., Kirby, I., Keeling, J., Ross, C.K., Larder, B.A., Stuart, D.I., Stammers, D.K.
      (1998) Proc Natl Acad Sci U S A 95: 9518
    • Continuous and discontinuous changes in the unit cell of HIV-1 reverse transcriptase crystals on dehydration
      Esnouf, R.M., Ren, J., Garman, E., Somers, D.O., Ross, C.K., Jones, E.Y., Stammers, D.K., Stuart, D.I.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 938
    • Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this non-nucleoside inhibitor
      Esnouf, R.M., Ren, J., Hopkins, A.L., Ross, C.K., Jones, E.Y., Stammers, D.K., Stuart, D.I.
      (1997) Proc Natl Acad Sci U S A 94: 3984
    • Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors
      Hopkins, A.L., Ren, J., Esnouf, R.M., Willcox, B.E., Jones, E.Y., Ross, C.K., Miyasaka, T., Walker, R.T., Tanaka, H., Stammers, D.K., Stuart, D.I.
      (1996) J Med Chem 39: 1589
    • The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design
      Ren, J., Esnouf, R.M., Hopkins, A.L., Ross, C.K., Jones, E.Y., Stammers, D.K., Stuart, D.I.
      (1995) Structure 3: 915
    • High Resolution Structures of HIV-1 RT From Four RT-inhibitor Complexes
      Ren, J., Esnouf, R.M., Garman, E., Somers, D.O., Ross, C.K., Kirby, I., Keeling, J., Darby, G., Jones, E.Y., Stuart, D.I., Stammers, D.K.
      (1995) Nat Struct Biol 2: 293
    • Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-nucleoside Inhibitors
      Esnouf, R.M., Ren, J., Ross, C.K., Jones, E.Y., Stammers, D.K., Stuart, D.I.
      (1995) Nat Struct Biol 2: 303
    • Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 Angstrom Resolution
      Stammers, D.K., Somers, D.O., Ross, C.K., Kirby, I., Ray, P.H., Wilson, J.E., Norman, M., Ren, J., Esnouf, R.M., Garman, E., Jones, E.Y., Stuart, D.I.
      (1994) J Mol Biol 242: 586

    Organizational Affiliation

    Laboratory of Molecular Biophysics, Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (A-CHAIN) A560Human immunodeficiency virus 1Mutation(s): 1 
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)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASE (B-CHAIN) B440Human immunodeficiency virus 1Mutation(s): 0 
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)
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
612
Query on 612

Download Ideal Coordinates CCD File 
A
6-(cyclohexylsulfanyl)-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione
C16 H26 N2 O3 S
JKXLRLDPSLZEDD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.8α = 90
b = 109.5β = 90
c = 71.7γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Non-polymer description