Crystal structure of L100I mutant HIV-1 reverse transcriptase in complex with nevirapine

Experimental Data Snapshot

  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 

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This is version 1.2 of the entry. See complete history


Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to 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: 569-578

  • DOI: 10.1016/j.jmb.2003.12.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Leu100Ile, Val106Ala and Val108Ile are mutations in HIV-1 reverse transcriptase (RT) that are observed in the clinic and give rise to resistance to certain non-nucleoside inhibitors (NNRTIs) including the first-generation drug nevirapine. In order to ...

    Leu100Ile, Val106Ala and Val108Ile are mutations in HIV-1 reverse transcriptase (RT) that are observed in the clinic and give rise to resistance to certain non-nucleoside inhibitors (NNRTIs) including the first-generation drug nevirapine. In order to investigate structural mechanisms of resistance for different NNRTI classes we have determined six crystal structures of mutant RT-inhibitor complexes. Val108 does not have direct contact with nevirapine in wild-type RT and in the RT(Val108Ile) complex the biggest change observed is at the distally positioned Tyr181 which is > 8 A from the mutation site. Thus in contrast to most NNRTI resistance mutations RT(Val108Ile) appears to act via an indirect mechanism which in this case is through alterations of the ring stacking interactions of the drug particularly with Tyr181. Shifts in side-chain and inhibitor positions compared to wild-type RT are observed in complexes of nevirapine and the second-generation NNRTI UC-781 with RT(Leu100Ile) and RT(Val106Ala), leading to perturbations in inhibitor contacts with Tyr181 and Tyr188. Such perturbations are likely to be a factor contributing to the greater loss of binding for nevirapine compared to UC-781 as, in the former case, a larger proportion of binding energy is derived from aromatic ring stacking of the inhibitor with the tyrosine side-chains. The differing resistance profiles of first and second generation NNRTIs for other drug resistance mutations in RT may also be in part due to this indirect mechanism.

    Related Citations: 
    • 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.,Suginoto, H.,Stuart, D.I.,Stammers, D.K.
      (2000) J.Biol.Chem. 275: 14316
    • 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
    • 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
    • 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
    • Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 A 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
    • Structural Basis for the Resilience of Efavirenz (Dmp-266) to Drug Resistance 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
    • 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
    • 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
    • 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
    • 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.,Stammers, D.K.
      (1998) Biochemistry 37: 14394
    • Crystallographic Analysis of the Binding Modes of Thiazoloisoindolinone Non-Nucleoside 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
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
560Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Reverse transcriptase
440Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 1 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on NVP

Download SDF File 
Download CCD File 
C15 H14 N4 O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Query on CSD
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NEVEC50: 20 - >7500 nM (99) BINDINGDB
NEVIC50: 2.6 - 23000 nM (99) BINDINGDB
NEVKi: 400 - 36000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Resolution: 3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 139.800α = 90.00
b = 115.500β = 90.00
c = 66.000γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance