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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structures of tyr188leu mutant and wild-Type HIV-1 reverse transcriptase complexed with the non-Nucleoside inhibitor hby 097: inhibitor flexibility is a useful design feature for reducing drug resistance.
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Authors
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Y.Hsiou,
K.Das,
J.Ding,
A.D.Clark,
J.P.Kleim,
M.Rösner,
I.Winkler,
G.Riess,
S.H.Hughes,
E.Arnold.
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Ref.
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J Mol Biol, 1998,
284,
313-323.
[DOI no: ]
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PubMed id
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Abstract
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The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097
(S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui
noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse
transcriptase (RT) and of HIV-1 infection in cell culture. HBY 097 selects for
unusual drug-resistance mutations in HIV-1 RT (e.g. Gly190Glu) when compared
with other non-nucleoside RT inhibitors (NNRTIs), such as nevirapine, alpha-APA
and TIBO. We have determined the structure of HBY 097 complexed with wild-type
HIV-1 RT at 3.1 A resolution. The HIV-1 RT/HBY 097 structure reveals an overall
inhibitor geometry and binding mode differing significantly from RT/NNRTI
structures reported earlier, in that HBY 097 does not adopt the usual
butterfly-like shape. We have determined the structure of the Tyr188Leu HIV-1 RT
drug-resistant mutant in complex with HBY 097 at 3.3 A resolution. HBY 097 binds
to the mutant RT in a manner similar to that seen in the wild-type RT/HBY 097
complex, although there are some repositioning and conformational alterations of
the inhibitor. Conformational changes of the structural elements forming the
inhibitor-binding pocket, including the orientation of some side-chains, are
observed. Reduction in the size of the 188 side-chain and repositioning of the
Phe227 side-chain increases the volume of the binding cavity in the Tyr188Leu
HIV-1 RT/HBY 097 complex. Loss of important protein-inhibitor interactions may
account for the reduced potency of HBY 097 against the Tyr188Leu HIV-1 RT
mutant. The loss of binding energy may be partially offset by additional
contacts resulting from conformational changes of the inhibitor and nearby amino
acid residues. This would suggest that inhibitor flexibility can help to
minimize drug resistance.
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Figure 1.
Figure 1. Diagram of HBY 097 (a quinoxaline derivative)
contacts with protein residues around the NNIBP in both (a)
wild-type HIV-1 RT/HBY 097 and (b) Tyr188Leu mutant HIV-1 RT/HBY
097 complexes. Distances (  slant
3.6 Å) between protein and inhibitor atoms are indicated.
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Figure 4.
Figure 4. (a) Stereoview of a difference Fourier m(F[obs] -
F[calc]) map showing the electron density of HBY 097 in the
wild-type HIV-1 RT/HBY 097 complex. The map is calculated at 3.1
Å resolution with 2s contours (in magenta). The phases
were computed from the protein model prior to inclusion of the
inhibitor. The green density corresponds to the difference
Fourier map (3.7 Å resolution) between HBY 097 and S-0483
complexed with wild-type HIV-1 RT (bromine in S-0483 replaces
the methoxy group of HBY 097), contoured at the 5s level,
showing the position of the bromine atom and confirming the
orientation and placement of the inhibitor. Difference Fourier
2mF[obs] - F[calc] map at 3.3 Å resolution, contoured at
1.2s, (b) of the Tyr188Leu mutant HIV-1 RT/HBY 097 complex at
the NNIBP region in p66 showing the absence of any density for
the side-chain of Leu188; clear density for HBY 097 is seen in
the binding pocket; and of a (c) similar region in the p51
subunit, showing clear electron density for the side-chain at
Leu188.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
284,
313-323)
copyright 1998.
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Secondary reference #1
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Title
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Crystal structures of 8-Cl and 9-Cl tibo complexed with wild-Type HIV-1 rt and 8-Cl tibo complexed with the tyr181cys HIV-1 rt drug-Resistant mutant.
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Authors
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K.Das,
J.Ding,
Y.Hsiou,
A.D.Clark,
H.Moereels,
L.Koymans,
K.Andries,
R.Pauwels,
P.A.Janssen,
P.L.Boyer,
P.Clark,
R.H.Smith,
M.B.Kroeger smith,
C.J.Michejda,
S.H.Hughes,
E.Arnold.
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Ref.
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J Mol Biol, 1996,
264,
1085-1100.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Chemical structures
with the numbering scheme used
and distances (E3.6 Å ) between
atoms of the TIBO inhibitor and of
the amino acid residues of the
NNIBP for: (a) 8-Cl TIBO (R86183,
tivirapine) complexed with wild-
type HIV-1 RT; (b) 8-Cl TIBO
complexed with Tyr181Cys mutant
HIV-1 RT; and (c) 9-Cl TIBO
(R82913) complexed with wild-type
HIV-1 RT. An NNIBP residue is
shown only if atoms of that residue
are E3.6 Å from an inhibitor atom
with the exception of Cys181 in (b).
The wings I and II portions of the
inhibitors in the butterfly-like anal-
ogy for NNRTIs (Ding et al., 1995a)
are indicated here and in sub-
sequent Figures by Roman nu-
merals I and II. The dotted line in (a)
indicates the subdivision of atoms
between wings I and II.
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Figure 5.
Figure 5. A stereoview of the superposition (based on the C
a
atoms of the b6-b10-b9 sheet) of the HIV-1 RT/DNA/Fab
complex structure (in gray) (Jacobo-Molina et al., 1993) on the HIV-1 RT/9-Cl TIBO complex structure (in cyan) in the
regions near the NNIBP and the polymerase active site showing the disposition of the b12-b13-b14 sheet containing
the primer grip. Bound 9-Cl TIBO in the HIV-1 RT/9-Cl TIBO complex is shown in gold and the two 3'-terminal
nucleotides 17 and 18 of the primer strand in the HIV-1 RT/DNA/Fab complex are shown with a yellow ball-and-stick
model. The broken line represents interactions between the primer grip and the primer terminal phosphate in the HIV-1
RT/DNA/Fab complex and the arrow indicates the movement of the primer grip that accompanies NNRTI binding.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Targeting HIV reverse transcriptase for anti-Aids drug design: structural and biological considerations for chemotherapeutic strategies.
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Authors
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E.Arnold,
K.Das,
J.Ding,
P.N.Yadav,
Y.Hsiou,
P.L.Boyer,
S.H.Hughes.
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Ref.
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Drug Des Discov, 1996,
13,
29-47.
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PubMed id
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Secondary reference #3
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Title
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Structure of unliganded HIV-1 reverse transcriptase at 2.7 a resolution: implications of conformational changes for polymerization and inhibition mechanisms.
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Authors
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Y.Hsiou,
J.Ding,
K.Das,
A.D.Clark,
S.H.Hughes,
E.Arnold.
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Ref.
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Structure, 1996,
4,
853-860.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Superposition of (a) unliganded RT and RT–DNA–Fab
complex and (b) unliganded RT and RT–α-APA
(α-anilinophenylacetamide) complex based on 89 Cα atoms in the
p66 palm subdomain, including the β6–β10–β9 region. The
unliganded RT is shown in red, RT–α-APA in blue, and
RT–DNA–Fab in green. A comparison of the two superpositions
reveals that NNRTI binding appears to be accompanied by a
long-range distortion that is coupled with a hinge motion
(indicated by curved arrows) between the β6–β10–β9 and
β12–β13–β14 sheets at the p66 palm subdomain (within the
circle). The different positions of the thumb in different HIV-1
RT structures supports the idea that this subdomain could play
a role during polymerization. Figure 3. Superposition of (a)
unliganded RT and RT–DNA–Fab complex and (b) unliganded RT
and RT–α-APA (α-anilinophenylacetamide) complex based on 89
Cα atoms in the p66 palm subdomain, including the
β6–β10–β9 region. The unliganded RT is shown in red,
RT–α-APA in blue, and RT–DNA–Fab in green. A comparison
of the two superpositions reveals that NNRTI binding appears to
be accompanied by a long-range distortion that is coupled with a
hinge motion (indicated by curved arrows) between the
β6–β10–β9 and β12–β13–β14 sheets at the p66 palm
subdomain (within the circle). The different positions of the
thumb in different HIV-1 RT structures supports the idea that
this subdomain could play a role during polymerization.
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Figure 4.
Figure 4. Stereoview of a portion of a (2mF[obs]–F[calc])
difference Fourier map at the p66 connection subdomain, at 2.7
å resolution. The phases were computed from the current
atomic model and the map is contoured at 1.4σ. The side chain
and the carboxyl groups are well defined in the electron density
map. Figure 4. Stereoview of a portion of a
(2mF[obs]–F[calc]) difference Fourier map at the p66
connection subdomain, at 2.7 å resolution. The phases were
computed from the current atomic model and the map is contoured
at 1.4σ. The side chain and the carboxyl groups are well
defined in the electron density map.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #4
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Title
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Structure of HIV-1 reverse transcriptase in a complex with the non-Nucleoside inhibitor alpha-Apa r 95845 at 2.8 a resolution.
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Authors
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J.Ding,
K.Das,
C.Tantillo,
W.Zhang,
A.D.Clark,
S.Jessen,
X.Lu,
Y.Hsiou,
A.Jacobo-Molina,
K.Andries.
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Ref.
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Structure, 1995,
3,
365-379.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. (a) Stereoview of difference Fourier maps showing the
fit of α-APA into the electron density. The α-APA coordinates
correspond to the current refined model. The green map is the
difference Fourier map at 3.5 å resolution between the
HIV-1 RT/α-APA R 95845 (dibrominated) complex and the HIV-1
RT/α-APA R 90385 (dichlorinated) complex contoured at a 10σ
level which revealed the positions of two bromine atoms. The
blue map is the mF[o]–F[c] difference Fourier map at 3.0
å resolution calculated from a model before α-APA was
included in the refinement; the phases were computed from the
back-transformation of electron density averaged from three
HIV-1 RT/inhibitor complexes; the map is contoured at 1.5σ. (b)
Stereoview of a portion of a 2mF[o]–F[c] difference Fourier
map at 2.8 å resolution in the region around the
non-nucleoside inhibitor-binding pocket showing the α-APA
inhibitor and some of the nearby amino acid residues. The phases
were computed from the current atomic model (R=0.255) and the
map is contoured at 1.2σ. Figure 2. (a) Stereoview of
difference Fourier maps showing the fit of α-APA into the
electron density. The α-APA coordinates correspond to the
current refined model. The green map is the difference Fourier
map at 3.5 å resolution between the HIV-1 RT/α-APA R
95845 (dibrominated) complex and the HIV-1 RT/α-APA R 90385
(dichlorinated) complex contoured at a 10σ level which revealed
the positions of two bromine atoms. The blue map is the
mF[o]–F[c] difference Fourier map at 3.0 å resolution
calculated from a model before α-APA was included in the
refinement; the phases were computed from the
back-transformation of electron density averaged from three
HIV-1 RT/inhibitor complexes; the map is contoured at 1.5σ. (b)
Stereoview of a portion of a 2mF[o]–F[c] difference Fourier
map at 2.8 å resolution in the region around the
non-nucleoside inhibitor-binding pocket showing the α-APA
inhibitor and some of the nearby amino acid residues. The phases
were computed from the current atomic model (R=0.255) and the
map is contoured at 1.2σ.
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Figure 4.
Figure 4. Close-up of the non-nucleoside inhibitor-binding
pocket in the structure of the HIV-1 RT/α-APA complex looking
through a putative entrance to the pocket, showing interactions
between α-APA and nearby amino acid residues. α-APA is shown
in purple as a ball-and-stick model with carbons purple,
nitrogens cyan, oxygens red and bromines magenta. The β7–β8
portion of p51 has a dashed outline. The side chains are shown
for the amino acid residues that make close contacts with α-APA
(in green), and for the three essential aspartic acid residues
D110, D185 and D186 (in red) at the polymerase active site.
Dashed lines indicate connections between the side chains and
the β-strands. Figure 4. Close-up of the non-nucleoside
inhibitor-binding pocket in the structure of the HIV-1 RT/α-APA
complex looking through a putative entrance to the pocket,
showing interactions between α-APA and nearby amino acid
residues. α-APA is shown in purple as a ball-and-stick model
with carbons purple, nitrogens cyan, oxygens red and bromines
magenta. The β7–β8 portion of p51 has a dashed outline. The
side chains are shown for the amino acid residues that make
close contacts with α-APA (in green), and for the three
essential aspartic acid residues D110, D185 and D186 (in red) at
the polymerase active site. Dashed lines indicate connections
between the side chains and the β-strands.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #5
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Title
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Structure of HIV-1 rt/tibo r 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors.
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Authors
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J.Ding,
K.Das,
H.Moereels,
L.Koymans,
K.Andries,
P.A.Janssen,
S.H.Hughes,
E.Arnold.
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Ref.
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Nat Struct Biol, 1995,
2,
407-415.
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PubMed id
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Secondary reference #6
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Title
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Locations of anti-Aids drug binding sites and resistance mutations in the three-Dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance.
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Authors
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C.Tantillo,
J.Ding,
A.Jacobo-Molina,
R.G.Nanni,
P.L.Boyer,
S.H.Hughes,
R.Pauwels,
K.Andries,
P.A.Janssen,
E.Arnold.
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Ref.
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J Mol Biol, 1994,
243,
369-387.
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PubMed id
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Secondary reference #7
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Title
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Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-Stranded DNA at 3.0 a resolution shows bent DNA.
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Authors
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A.Jacobo-Molina,
J.Ding,
R.G.Nanni,
A.D.Clark,
X.Lu,
C.Tantillo,
R.L.Williams,
G.Kamer,
A.L.Ferris,
P.Clark.
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Ref.
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Proc Natl Acad Sci U S A, 1993,
90,
6320-6324.
[DOI no: ]
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PubMed id
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