1S1X

Crystal structure of V108I mutant HIV-1 reverse transcriptase in complex with nevirapine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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:  
    1S1V, 1S1U, 1S1T, 1S1X, 1S1W

  • 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 investigate structural mechanisms of resistance for different NNRTI classes we have determined six crystal structures of mutant RT-inhibitor complexes ...

    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: 
    • 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-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
    • 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
    • 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
    • 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 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
    • 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
    • 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 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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Reverse transcriptaseA560Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: 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
Reverse transcriptaseB440Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVP
Query on NVP

Download Ideal Coordinates CCD File 
C [auth A]11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE
C15 H14 N4 O
NQDJXKOVJZTUJA-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 %)
NEVEC50:  380   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVIC50:  23000   nM  BindingDB
NEVIC50:  101   nM  BindingDB
NEVKi:  36000   nM  BindingDB
NEVIC50:  100   nM  BindingDB
NEVEC50:  250   nM  BindingDB
NEVIC50:  60   nM  BindingDB
NEVIC50:  20000   nM  BindingDB
NEVIC50:  11800   nM  BindingDB
NEVIC50:  11300   nM  BindingDB
NEVIC50:  13000   nM  BindingDB
NEVKi:  18000   nM  BindingDB
NEVIC50:  14000   nM  BindingDB
NEVIC50:  5750   nM  BindingDB
NEVIC50:  5500   nM  BindingDB
NEVIC50:  6440   nM  BindingDB
NEVIC50:  6000   nM  BindingDB
NEVIC50:  6650   nM  BindingDB
NEVIC50:  1700   nM  BindingDB
NEVIC50:  3930   nM  BindingDB
NEVIC50:  3800   nM  BindingDB
NEVKi:  400   nM  BindingDB
NEVIC50:  4848   nM  BindingDB
NEVIC50:  2600   nM  BindingDB
NEVIC50:  2800   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  3200   nM  BindingDB
NEVIC50:  3000   nM  BindingDB
NEVIC50:  3100   nM  BindingDB
NEVIC50:  3500   nM  BindingDB
NEVEC50:  7500   nM  BindingDB
NEVIC50:  1850   nM  BindingDB
NEVEC50:  26   nM  BindingDB
NEVIC50:  690   nM  BindingDB
NEVIC50:  1900   nM  BindingDB
NEVIC50:  2110   nM  BindingDB
NEVIC50:  1300   nM  BindingDB
NEVIC50:  1480   nM  BindingDB
NEVEC50:  20   nM  BindingDB
NEVEC50:  3900   nM  BindingDB
NEVKi:  2000   nM  BindingDB
NEVIC50:  1100   nM  BindingDB
NEVIC50:  640   nM  BindingDB
NEVIC50:  700   nM  BindingDB
NEVIC50:  860   nM  BindingDB
NEVEC50:  100   nM  BindingDB
NEVIC50:  500   nM  BindingDB
NEVKi:  10000   nM  BindingDB
NEVEC50:  110   nM  BindingDB
NEVIC50:  2.5999999046325684   nM  BindingDB
NEVIC50:  600   nM  BindingDB
NEVIC50:  320   nM  BindingDB
NEVEC50:  70   nM  BindingDB
NEVIC50:  80   nM  BindingDB
NEVKi:  7000   nM  BindingDB
NEVIC50:  84   nM  BindingDB
NEVKi:  9000   nM  BindingDB
NEVIC50:  430   nM  BindingDB
NEVIC50:  230   nM  BindingDB
NEVEC50:  52   nM  BindingDB
NEVEC50:  53   nM  BindingDB
NEVIC50:  250   nM  BindingDB
NEVIC50:  270   nM  BindingDB
NEVIC50:  300   nM  BindingDB
NEVIC50:  170   nM  BindingDB
NEVIC50:  180   nM  BindingDB
NEVIC50:  200   nM  BindingDB
NEVEC50:  30   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.4α = 90
b = 109β = 90
c = 72.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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