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PDBsum entry 4g1q
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Transferase, hydrolase/inhibitor
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PDB id
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4g1q
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References listed in PDB file
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Key reference
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Title
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Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.
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Authors
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D.G.Kuroda,
J.D.Bauman,
J.R.Challa,
D.Patel,
T.Troxler,
K.Das,
E.Arnold,
R.M.Hochstrasser.
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Ref.
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Nat Chem, 2013,
5,
174-181.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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Secondary reference #1
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Title
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High-Resolution structures of HIV-1 reverse transcriptase/tmc278 complexes: strategic flexibility explains potency against resistance mutations.
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Authors
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K.Das,
J.D.Bauman,
A.D.Clark,
Y.V.Frenkel,
P.J.Lewi,
A.J.Shatkin,
S.H.Hughes,
E.Arnold.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
1466-1471.
[DOI no: ]
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PubMed id
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Figure 2.
Binding mode of TMC278 to HIV-1 RT. (A) Interactions of
TMC278 (gray) with NNRTI-binding pocket residues (in yellow).
(B) The molecular surface (orange) defines the hydrophobic
tunnel that accommodates the cyanovinyl group of TMC278.
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Figure 4.
Comparison of L100I/K103N mutant RT (orange side
chains)/TMC278 (cyan) structure with the wild-type RT (yellow
side chains)/TMC278 (gray) structures reveals wiggling (A) and
jiggling (B) of TMC278.
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Secondary reference #2
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Title
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Hiv-1 reverse transcriptase complex with DNA and nevirapine reveals non-Nucleoside inhibition mechanism.
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Authors
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K.Das,
S.E.Martinez,
J.D.Bauman,
E.Arnold.
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Ref.
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Nat Struct Biol, 2012,
19,
253-259.
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PubMed id
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Secondary reference #3
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Title
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Crystal engineering of HIV-1 reverse transcriptase for structure-Based drug design.
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Authors
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J.D.Bauman,
K.Das,
W.C.Ho,
M.Baweja,
D.M.Himmel,
A.D.Clark,
D.A.Oren,
P.L.Boyer,
S.H.Hughes,
A.J.Shatkin,
E.Arnold.
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Ref.
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Nucleic Acids Res, 2008,
36,
5083-5092.
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PubMed id
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Secondary reference #4
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Title
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Crystal structures of clinically relevant lys103asn/tyr181cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-Nucleoside inhibitor hby 097.
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Authors
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K.Das,
S.G.Sarafianos,
A.D.Clark,
P.L.Boyer,
S.H.Hughes,
E.Arnold.
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Ref.
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J Mol Biol, 2007,
365,
77-89.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Effects of the two mutations (Lys103Asn and
Tyr181Cys) on the structure of unliganded HIV-1 RT. (a) A stereo
view of the NNIBP region of the double mutant RT/ATP structure.
The composite simulated annealing omit map (2|F[o]|–|F[c]|)
electron density (cyan) contoured at 1.2σ defines the
coordination of a Na ion at the NNIBP region; OW1 and OW2 are
two water molecules. (b) The NNIBP region of the double mutant
(Lys103Asn/Tyr181Cys) HIV-1 RT. The mutated amino acids have
altered interactions with the surrounding amino acids. (c) The
NNIBP region of the wild type unliganded HIV-1 RT structure.^13
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Figure 2.
Figure 2. Binding mode of HBY 097 to the
Lys103Asn/Tyr181Cys double mutant RT. (a) Stereo view of the
(2|F[o]|–|F[c]|) electron density (contoured at 1.2σ)
covering HBY 097 (cyan) and Cys181 (magenta). The dotted line
represents the hydrogen bond between the thiol group of Cys181
and HBY 097. Electrostatic potential surface^62 showing the
NNIBP region of (b) the double mutant RT/HBY 097 and (c)
wild-type RT/HBY 097^13 structures.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #5
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Title
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Roles of conformational and positional adaptability in structure-Based design of tmc125-R165335 (etravirine) and related non-Nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-Type and drug-Resistant HIV-1 variants.
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Authors
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K.Das,
A.D.Clark,
P.J.Lewi,
J.Heeres,
M.R.De jonge,
L.M.Koymans,
H.M.Vinkers,
F.Daeyaert,
D.W.Ludovici,
M.J.Kukla,
B.De corte,
R.W.Kavash,
C.Y.Ho,
H.Ye,
M.A.Lichtenstein,
K.Andries,
R.Pauwels,
M.P.De béthune,
P.L.Boyer,
P.Clark,
S.H.Hughes,
P.A.Janssen,
E.Arnold.
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Ref.
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J Med Chem, 2004,
47,
2550-2560.
[DOI no: ]
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PubMed id
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