1TL3

Crystal structure of hiv-1 reverse transcriptase in complex with gw450557


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of non-nucleoside inhibitors of HIV-1 reverse transcriptase with improved drug resistance properties. 1.

Hopkins, A.L.Ren, J.Milton, J.Hazen, R.J.Chan, J.H.Stuart, D.I.Stammers, D.K.

(2004) J Med Chem 47: 5912-5922

  • DOI: 10.1021/jm040071z
  • Primary Citation of Related Structures:  
    1TKZ, 1TKT, 1TL3, 1TL1

  • PubMed Abstract: 
  • We have used a structure-based approach to design a novel series of non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Detailed analysis of a wide range of crystal structures of HIV-1 RT-NNRTI complexes together with data on drug resistance mutations ha ...

    We have used a structure-based approach to design a novel series of non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Detailed analysis of a wide range of crystal structures of HIV-1 RT-NNRTI complexes together with data on drug resistance mutations has identified factors important for tight binding of inhibitors and resilience to mutations. Using this approach we have designed and synthesized a novel series of quinolone NNRTIs. Crystal structure analysis of four of these compounds in complexes with HIV-1 RT confirms the predicted binding modes. Members of this quinolone series retain high activity against the important resistance mutations in RT at Tyr181Cys and Leu100Ile.


    Related Citations: 
    • Design of Non-Nucleoside Inhibitors of HIV-1 Revers Transcriptase with Improved Drug Resistance Propert Part II.
      Freeman, G.A., Andrews III, C.W., Hopkins, A.L., Lowell, G.S., Schaller, L.T., Cowan, J.L., Gonzales, S.S., Koszalka, G.W., Hazen, R.J., Boone, L.R., Ferris, R.G., Creech, K.L., Short, G.B., A., Rober S., Weaver, K., Reynolds, D.J., Milton, J., Ren, J., Stuart, D.I., Stammers, D.K., Chan, J.H.
      () To be published --: --
    • Crystal Structures of HIV-1 Reverse Transcriptases at Codons 100, 106 and 108 and Mechanisms of Resist Non-Nucleoside Inhibitors
      Ren, J., Nichols, C.E., Chamberlain, P.P., Weaver, K.L., Short, S.A., Stammers, D.K.
      (2004) J Mol Biol 336: 569
    • Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215
      Chamberlain, P.P., Ren, J., Nichols, C.E., Douglas, L., Lennerstrand, J., Larder, B.A., Stuart, D.I., Stammers, D.K.
      (2002) J Virol 76: 10015
    • Structural Mechanisms of Drug Resistance for Mutations at Codons 181 and 188 in HIV-1 Reverse Transcriptase and the Improved Resilience of Second Generation Non-Nucleoside Inhibitors
      Ren, J., Nichols, C., Bird, L., Chamberlain, P., Weaver, K.L., Short, S.A., Stuart, D.I., Stammers, D.K.
      (2001) J Mol Biol 312: 795
    • 2-Amino-6-Arylsulfonylbenzonitriles as Non-Nucleosi Transcriptase Inhibitors of HIV-1
      Chan, J.H., Hong, J.S., Hunter III, R.N., Orr, G.F., Cowan, J.R., Sherman, D.B., Sparks, S.M., Reitter, B.E., Hazen, C.W., Andrews III, R.J., St Clair, M., Boone, L.R., Ferris, R.G., Roberts, K.L., Cree, G.B., Short, S.A., Weaver, K., Ott, R.J., Ren, J., Hopkins, A., Stuart, D.I., Stammers, D.K.
      (2001) J Med Chem 44: 1866
    • Structural Basis for the Resilience of Efavirenz (Dmp-266) to Drug Resistant Mutations in HIV-1 Reverse Transcriptase
      Ren, J., Milton, J., Weaver, K.L., Short, S.A., Stuart, D.I., Stammers, D.K.
      (2000) Structure 8: 1089
    • Binding of the Second Generattion 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., Suginoto, H., Stuart, D.I., Stammers, D.K.
      (2000) J Biol Chem 275: 14316
    • 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., 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., 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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pol polyprotein, Reverse transcriptase, Chain AA560Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: Name=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)
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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pol polyprotein, Reverse transcriptase, Chain BB440Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: Name=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)
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H20
Query on H20

Download CCD File 
A
6-CHLORO-4-(CYCLOHEXYLOXY)-3-ISOPROPYLQUINOLIN-2(1H)-ONE
C18 H22 Cl N O2
OQCFORGSZJSAEL-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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 %)
H20IC50 :  630   nM  PDBBind
H20IC50:  2500   nM  BindingDB
H20IC50:  630   nM  BindingDB
H20IC50:  1960   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 115.2β = 90
c = 65.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Database references