1EP4

Crystal structure of HIV-1 reverse transcriptase in complex with S-1153


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of the second generation non-nucleoside inhibitor S-1153 to HIV-1 reverse transcriptase involves extensive main chain hydrogen bonding.

Ren, J.Nichols, C.Bird, L.E.Fujiwara, T.Sugimoto, H.Stuart, D.I.Stammers, D.K.

(2000) J Biol Chem 275: 14316-14320

  • DOI: 10.1074/jbc.275.19.14316
  • Primary Citation of Related Structures:  
    1EP4

  • PubMed Abstract: 
  • S-1153 (AG1549) is perhaps the most promising non-nucleoside inhibitor of HIV-1 reverse transcriptase currently under development as a potential anti-AIDS drug, because it has a favorable profile of resilience to many drug resistance mutations. We ha ...

    S-1153 (AG1549) is perhaps the most promising non-nucleoside inhibitor of HIV-1 reverse transcriptase currently under development as a potential anti-AIDS drug, because it has a favorable profile of resilience to many drug resistance mutations. We have determined the crystal structure of S-1153 in a complex with HIV-1 reverse transcriptase. The complex possesses some novel features, including an extensive network of hydrogen bonds involving the main chain of residues 101, 103, and 236 of the p66 reverse transcriptase subunit. Such interactions are unlikely to be disrupted by side chain mutations. The reverse transcriptase/S-1153 complex suggests different ways in which resilience to mutations in the non-nucleoside inhibitors of reverse transcriptase binding site can be achieved.


    Related Citations: 
    • Phenethylthiazolylthiourea (PETT) Non-nucleoside Inhibitors of HIV-1 and HIV-2 Reverse Transcriptases: Structural and Biochemical Analyses
      Ren, J., Diprose, J., Warren, J., Esnouf, R.M., Bird, L.E., Ikemizu, S., Slater, M., Milton, J., Balzarini, J., Stuart, D.I., Stammers, D.K.
      (2000) J Biol Chem 275: 5633
    • Crystallographic Analysis of the Binding Modes of Non-nucleoside Thiazoloisoindolinone Inhibitors to HIV-1 Reverse Transcriptase and Comparison with Modeling Studies
      Ren, J., Esnouf, R.M., Hopkins, A.L., Stuart, D.I., Stammers, D.K.
      (1999) J Med Chem 42: 3845
    • 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
    • Crystal Structures of Reverse Transcriptase in Complex with Carboxanilide Derivatives
      Ren, J., Esnouf, R.M., Hopkins, A.L., Warren, J., Balzarini, J., Stuart, D.I., Stammers, D.K.
      (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.F., 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
      L Hopkins, A., 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., K Stammers, D., 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

    Structural Biology Division, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEA560Human 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 REVERSE TRANSCRIPTASEB440Human 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
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S11
Query on S11

Download CCD File 
A
5-(3,5-DICHLOROPHENYL)THIO-4-ISOPROPYL-1-(PYRIDIN-4-YL-METHYL)-1H-IMIDAZOL-2-YL-METHYL CARBAMATE
C20 H20 Cl2 N4 O2 S
YQXCVAGCMNFUMQ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S11IC50:  47   nM  BindingDB
S11IC50:  61   nM  BindingDB
S11IC50:  68   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.330 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.7α = 90
b = 118β = 90
c = 67.3γ = 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: 2000-09-27
    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: Structure summary