1JKH

CRYSTAL STRUCTURE OF Y181C MUTANT HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DMP-266(EFAVIRENZ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.Short, S.Stuart, D.I.Stammers, D.K.

(2001) J.Mol.Biol. 312: 795-805

  • DOI: 10.1006/jmbi.2001.4988
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mutations at either Tyr181 or Tyr188 within HIV-1 reverse transcriptase (RT) give high level resistance to many first generation non-nucleoside inhibitors (NNRTIs) such as the anti-AIDS drug nevirapine. By comparison second generation inhibitors, for ...

    Mutations at either Tyr181 or Tyr188 within HIV-1 reverse transcriptase (RT) give high level resistance to many first generation non-nucleoside inhibitors (NNRTIs) such as the anti-AIDS drug nevirapine. By comparison second generation inhibitors, for instance the drug efavirenz, show much greater resilience to these mutations. In order to understand the structural basis for these differences we have determined a series of seven crystal structures of mutant RTs in complexes with first and second generation NNRTIs as well as one example of an unliganded mutant RT. These are Tyr181Cys RT (TNK-651) to 2.4 A, Tyr181Cys RT (efavirenz) to 2.6 A, Tyr181Cys RT (nevirapine) to 3.0 A, Tyr181Cys RT (PETT-2) to 3.0 A, Tyr188Cys RT (nevirapine) to 2.6 A, Tyr188Cys RT (UC-781) to 2.6 A and Tyr188Cys RT (unliganded) to 2.8 A resolution. In the two previously published structures of HIV-1 reverse transcriptase with mutations at 181 or 188 no side-chain electron density was observed within the p66 subunit (which contains the inhibitor binding pocket) for the mutated residues. In contrast the mutated side-chains can be seen in the NNRTI pocket for all seven structures reported here, eliminating the possibility that disordering contributes to the mechanism of resistance. In the case of the second generation compounds efavirenz with Tyr181Cys RT and UC-781 with Tyr188Cys RT there are only small rearrangements of either inhibitor within the binding site compared to wild-type RT and also for the first generation compounds TNK-651, PETT-2 and nevirapine with Tyr181Cys RT. For nevirapine with the Tyr188Cys RT there is however a more substantial movement of the drug molecule. We conclude that protein conformational changes and rearrangements of drug molecules within the mutated sites are not general features of these particular inhibitor/mutant combinations. The main contribution to drug resistance for Tyr181Cys and Tyr188Cys RT mutations is the loss of aromatic ring stacking interactions for first generation compounds, providing a simple explanation for the resilience of second generation NNRTIs, as such interactions make much less significant contribution to their binding.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 2-Amino-6-Arylsulfonylbenzonitriles as Non-Nucleoside Reverse 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.,Andrews III, C.W.,Hazen, R.J.,St Clair, M.,Boone, L.R.,Ferris, R.G.,Creech, K.L.,Roberts, 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Structural Biology Division, 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
HIV-1 RT, A-CHAIN
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
HIV-1 RT, B-CHAIN
B
440Human immunodeficiency virus type 1 group M subtype BMutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EFZ
Query on EFZ

Download SDF File 
Download CCD File 
A
(-)-6-CHLORO-4-CYCLOPROPYLETHYNYL-4-TRIFLUOROMETHYL-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-2-ONE
DMP-266; Efavirenz
C14 H9 Cl F3 N O2
XPOQHMRABVBWPR-ZDUSSCGKSA-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 %)
EFZIC50: 0.8 - 3400 nM (99) BINDINGDB
EFZEC50: 1 - 300 nM (99) BINDINGDB
EFZKi: 3 - 380 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 138.500α = 90.00
b = 109.000β = 90.00
c = 73.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-18
    Type: Non-polymer description