1TL1

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH GW451211


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 

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:  

  • 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: 
    • 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
    • 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.USA 95: 9518
    • 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.USA 94: 3984
    • 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 --: --
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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.Mol.Biol. 2: 293
    • 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
    • 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.,Sect.D 54: 938
    • 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
    • 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
    • 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
    • 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
    • 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.Mol.Biol. 2: 303


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pol polyprotein, Reverse transcriptase, Chain A
A
560Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pol polyprotein, Reverse transcriptase, Chain B
B
440Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
H18
Query on H18

Download SDF File 
Download CCD File 
A
6-CHLORO-4-(CYCLOHEXYLSULFINYL)-3-PROPYLQUINOLIN-2(1H)-ONE
C18 H22 Cl N O2 S
QRBUGQMJMFAHKS-HSZRJFAPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
H18IC50: 380 - 2380 nM (99) BINDINGDB
H18IC50: 380 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 137.500α = 90.00
b = 115.300β = 90.00
c = 65.400γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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