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* Residue conservation analysis
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PDB id:
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| Name: |
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Nucleotidyltransferase
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Title:
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High resolution structures of HIV-1 rt from four rt-inhibitor complexes
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Structure:
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HIV-1 reverse transcriptase. Chain: a. Synonym: HIV-1 rt. Engineered: yes. HIV-1 reverse transcriptase. Chain: b. Synonym: HIV-1 rt. Engineered: yes
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Source:
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Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: hxb2 isolate. Cell_line: 293. Gene: HIV-1 pol. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dimer (from
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Resolution:
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Authors:
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J.Ren,R.Esnouf,E.Garman,D.Somers,C.Ross,I.Kirby,J.Keeling,G.Darby, Y.Jones,D.Stuart,D.Stammers
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Key ref:
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J.Ren
et al.
(1995).
High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
Nat Struct Biol,
2,
293-302.
PubMed id:
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Date:
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19-Apr-95
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Release date:
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03-Apr-96
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PROCHECK
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Headers
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References
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Enzyme class 1:
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Chains A, B:
E.C.2.7.7.-
- ?????
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Enzyme class 2:
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Chains A, B:
E.C.2.7.7.49
- RNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 3:
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Chains A, B:
E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Enzyme class 4:
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Chains A, B:
E.C.3.1.-.-
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Enzyme class 5:
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Chains A, B:
E.C.3.1.13.2
- exoribonuclease H.
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Reaction:
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Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
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Enzyme class 6:
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Chains A, B:
E.C.3.1.26.13
- retroviral ribonuclease H.
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Enzyme class 7:
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Chains A, B:
E.C.3.4.23.16
- HIV-1 retropepsin.
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Reaction:
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Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Nat Struct Biol
2:293-302
(1995)
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PubMed id:
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High resolution structures of HIV-1 RT from four RT-inhibitor complexes.
|
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J.Ren,
R.Esnouf,
E.Garman,
D.Somers,
C.Ross,
I.Kirby,
J.Keeling,
G.Darby,
Y.Jones,
D.Stuart.
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ABSTRACT
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We have determined the structures of four complexes of HIV-1 reverse
transcriptase with non-nucleoside inhibitors, three fully refined at high
resolution. The highest resolution structure is of the RT-nevirapine complex
which has an R-factor of 0.186 and a root-mean-square bond length deviation of
0.015 A for all data to 2.2 A. The structures reveal a common mode of binding
for these chemically diverse compounds. The common features of binding are
largely hydrophobic interactions and arise from induced shape complementarity
achieved by conformational rearrangement of the enzyme and
conformational/configurational rearrangement of the compounds.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.Das,
S.E.Martinez,
J.D.Bauman,
and
E.Arnold
(2012).
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
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Nat Struct Mol Biol,
19,
253-259.
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PDB codes:
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L.Q.Al-Mawsawi,
and
N.Neamati
(2011).
Allosteric Inhibitor Development Targeting HIV-1 Integrase.
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ChemMedChem,
6,
228-241.
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|
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P.Decha,
P.Intharathep,
T.Udommaneethanakit,
P.Sompornpisut,
S.Hannongbua,
P.Wolschann,
and
V.Parasuk
(2011).
Theoretical studies on the molecular basis of HIV-1RT/NNRTIs interactions.
|
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J Enzyme Inhib Med Chem,
26,
29-36.
|
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|
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|
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A.J.Kandathil,
A.P.Joseph,
R.Kannangai,
N.Srinivasan,
O.C.Abraham,
S.A.Pulimood,
and
G.Sridharan
(2010).
HIV reverse transcriptase: Structural interpretation of drug resistant genetic variants from India.
|
| |
Bioinformation,
4,
36-45.
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H.Gatanaga,
H.Ode,
A.Hachiya,
T.Hayashida,
H.Sato,
M.Takiguchi,
and
S.Oka
(2010).
Impact of human leukocyte antigen-B*51-restricted cytotoxic T-lymphocyte pressure on mutation patterns of nonnucleoside reverse transcriptase inhibitor resistance.
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| |
AIDS,
24,
F15-F22.
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H.Gatanaga,
H.Ode,
A.Hachiya,
T.Hayashida,
H.Sato,
and
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(2010).
Combination of V106I and V179D polymorphic mutations in human immunodeficiency virus type 1 reverse transcriptase confers resistance to efavirenz and nevirapine but not etravirine.
|
| |
Antimicrob Agents Chemother,
54,
1596-1602.
|
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|
|
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J.J.Tan,
X.J.Cong,
L.M.Hu,
C.X.Wang,
L.Jia,
and
X.J.Liang
(2010).
Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection.
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Drug Discov Today,
15,
186-197.
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|
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K.A.Delviks-Frankenberry,
G.N.Nikolenko,
and
V.K.Pathak
(2010).
The "Connection" Between HIV Drug Resistance and RNase H.
|
| |
Viruses,
2,
1476-1503.
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|
|
|
|
|
K.Singh,
B.Marchand,
K.A.Kirby,
E.Michailidis,
and
S.G.Sarafianos
(2010).
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
|
| |
Viruses,
2,
606-638.
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|
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|
R.Hu,
F.Barbault,
F.Maurel,
M.Delamar,
and
R.Zhang
(2010).
Molecular dynamics simulations of 2-amino-6-arylsulphonylbenzonitriles analogues as HIV inhibitors: interaction modes and binding free energies.
|
| |
Chem Biol Drug Des,
76,
518-526.
|
|
|
|
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|
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R.K.Raju,
N.A.Burton,
and
I.H.Hillier
(2010).
Modelling the binding of HIV-reverse transcriptase and nevirapine: an assessment of quantum mechanical and force field approaches and predictions of the effect of mutations on binding.
|
| |
Phys Chem Chem Phys,
12,
7117-7125.
|
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|
|
|
|
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A.Ivetac,
and
J.A.McCammon
(2009).
Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations.
|
| |
J Mol Biol,
388,
644-658.
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D.H.Mahajan,
C.Pannecouque,
E.De Clercq,
and
K.H.Chikhalia
(2009).
Synthesis and studies of new 2-(coumarin-4-yloxy)-4,6-(substituted)-s-triazine derivatives as potential anti-HIV agents.
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Arch Pharm (Weinheim),
342,
281-290.
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J.Sanchez-Weatherby,
M.W.Bowler,
J.Huet,
A.Gobbo,
F.Felisaz,
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R.Moya,
J.Kadlec,
R.B.Ravelli,
and
F.Cipriani
(2009).
Improving diffraction by humidity control: a novel device compatible with X-ray beamlines.
|
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Acta Crystallogr D Biol Crystallogr,
65,
1237-1246.
|
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PDB codes:
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|
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N.R.El-Brollosy,
O.A.Al-Deeb,
A.A.El-Emam,
E.B.Pedersen,
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G.Collu,
G.Sanna,
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(2009).
Synthesis of novel uracil non-nucleoside derivatives as potential reverse transcriptase inhibitors of HIV-1.
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Arch Pharm (Weinheim),
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N.S.Sapre,
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N.Pancholi,
and
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(2009).
A group center overlap based approach for "3D QSAR" studies on TIBO derivatives.
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J Comput Chem,
30,
922-933.
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S.E.Nichols,
R.A.Domaoal,
V.V.Thakur,
J.Tirado-Rives,
K.S.Anderson,
and
W.L.Jorgensen
(2009).
Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures.
|
| |
J Chem Inf Model,
49,
1272-1279.
|
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|
|
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|
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S.G.Sarafianos,
B.Marchand,
K.Das,
D.M.Himmel,
M.A.Parniak,
S.H.Hughes,
and
E.Arnold
(2009).
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
|
| |
J Mol Biol,
385,
693-713.
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Y.M.Loksha,
E.B.Pedersen,
R.Loddo,
and
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(2009).
Synthesis and anti-HIV-1 activity of 1-substiuted 6-(3-cyanobenzoyl) and [(3-cyanophenyl)fluoromethyl]-5-ethyl-uracils.
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Arch Pharm (Weinheim),
342,
501-506.
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D.Grohmann,
V.Corradi,
M.Elbasyouny,
A.Baude,
F.Horenkamp,
S.D.Laufer,
F.Manetti,
M.Botta,
and
T.Restle
(2008).
Small molecule inhibitors targeting HIV-1 reverse transcriptase dimerization.
|
| |
Chembiochem,
9,
916-922.
|
|
|
|
|
|
|
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,
and
E.Arnold
(2008).
Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
|
| |
Nucleic Acids Res,
36,
5083-5092.
|
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PDB code:
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|
|
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|
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K.Das,
J.D.Bauman,
A.D.Clark,
Y.V.Frenkel,
P.J.Lewi,
A.J.Shatkin,
S.H.Hughes,
and
E.Arnold
(2008).
High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
|
| |
Proc Natl Acad Sci U S A,
105,
1466-1471.
|
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PDB codes:
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|
|
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|
M.L.Coté,
and
M.J.Roth
(2008).
Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase.
|
| |
Virus Res,
134,
186-202.
|
|
|
|
|
|
|
M.Radi,
C.Falciani,
L.Contemori,
E.Petricci,
G.Maga,
A.Samuele,
S.Zanoli,
M.Terrazas,
M.Castria,
A.Togninelli,
J.A.Esté,
I.Clotet-Codina,
M.Armand-Ugón,
and
M.Botta
(2008).
A multidisciplinary approach for the identification of novel HIV-1 non-nucleoside reverse transcriptase inhibitors: S-DABOCs and DAVPs.
|
| |
ChemMedChem,
3,
573-593.
|
|
|
|
|
|
|
N.S.Sapre,
S.Gupta,
N.Pancholi,
and
N.Sapre
(2008).
Molecular docking studies on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors.
|
| |
J Comput Aided Mol Des,
22,
69-80.
|
|
|
|
|
|
|
N.S.Sapre,
S.Gupta,
N.Pancholi,
and
N.Sapre
(2008).
Data mining using template-based molecular docking on tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone (TIBO) derivatives as HIV-1RT inhibitors.
|
| |
J Mol Model,
14,
1009-1021.
|
|
|
|
|
|
|
P.Srivab,
and
S.Hannongbua
(2008).
A study of the binding energies of efavirenz to wild-type and K103N/Y181C HIV-1 reverse transcriptase based on the ONIOM method.
|
| |
ChemMedChem,
3,
803-811.
|
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|
|
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|
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S.Liu,
E.A.Abbondanzieri,
J.W.Rausch,
S.F.Le Grice,
and
X.Zhuang
(2008).
Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates.
|
| |
Science,
322,
1092-1097.
|
|
|
|
|
|
|
Y.Lin,
X.Liu,
R.Yan,
J.Li,
C.Pannecouque,
M.Witvrouw,
and
E.De Clercq
(2008).
Synthesis and anti-HIV evaluation of novel 1,3-disubstituted thieno[3,2-c][1,2,6]thiadiazin-4(3H)-one 2,2-dioxides(TTDDs).
|
| |
Bioorg Med Chem,
16,
157-163.
|
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|
|
|
|
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B.N.Kelly,
S.Kyere,
I.Kinde,
C.Tang,
B.R.Howard,
H.Robinson,
W.I.Sundquist,
M.F.Summers,
and
C.P.Hill
(2007).
Structure of the antiviral assembly inhibitor CAP-1 complex with the HIV-1 CA protein.
|
| |
J Mol Biol,
373,
355-366.
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PDB codes:
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C.C.da Silva,
S.L.Cuffini,
S.N.Faudone,
A.P.Ayala,
and
J.Ellena
(2007).
Low-temperature study of a new nevirapine pseudopolymorph.
|
| |
Acta Crystallogr Sect E Struct Rep Online,
64,
o292.
|
|
|
|
|
|
|
G.Barreiro,
C.R.Guimarães,
I.Tubert-Brohman,
T.M.Lyons,
J.Tirado-Rives,
and
W.L.Jorgensen
(2007).
Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring.
|
| |
J Chem Inf Model,
47,
2416-2428.
|
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|
|
|
|
|
R.K.Rawal,
A.Kumar,
M.I.Siddiqi,
and
S.B.Katti
(2007).
Molecular docking studies on 4-thiazolidinones as HIV-1 RT inhibitors.
|
| |
J Mol Model,
13,
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|
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|
|
S.H.Yap,
C.W.Sheen,
J.Fahey,
M.Zanin,
D.Tyssen,
V.D.Lima,
B.Wynhoven,
M.Kuiper,
N.Sluis-Cremer,
P.R.Harrigan,
and
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(2007).
N348I in the connection domain of HIV-1 reverse transcriptase confers zidovudine and nevirapine resistance.
|
| |
PLoS Med,
4,
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|
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|
|
|
|
S.Yamazaki,
L.Tan,
G.Mayer,
J.S.Hartig,
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T.Restle,
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D.Grohmann,
H.G.Kräusslich,
J.Bajorath,
and
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(2007).
Aptamer displacement identifies alternative small-molecule target sites that escape viral resistance.
|
| |
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|
V.Hornak,
and
C.Simmerling
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Targeting structural flexibility in HIV-1 protease inhibitor binding.
|
| |
Drug Discov Today,
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|
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|
Y.El Safadi,
V.Vivet-Boudou,
and
R.Marquet
(2007).
HIV-1 reverse transcriptase inhibitors.
|
| |
Appl Microbiol Biotechnol,
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|
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|
D.M.Himmel,
S.G.Sarafianos,
S.Dharmasena,
M.M.Hossain,
K.McCoy-Simandle,
T.Ilina,
A.D.Clark,
J.L.Knight,
J.G.Julias,
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S.H.Hughes,
M.A.Parniak,
and
E.Arnold
(2006).
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
|
| |
ACS Chem Biol,
1,
702-712.
|
|
|
PDB code:
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|
|
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|
|
J.Ren,
C.E.Nichols,
A.Stamp,
P.P.Chamberlain,
R.Ferris,
K.L.Weaver,
S.A.Short,
and
D.K.Stammers
(2006).
Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138.
|
| |
FEBS J,
273,
3850-3860.
|
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|
PDB codes:
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|
|
R.A.Domaoal,
R.A.Bambara,
and
L.M.Demeter
(2006).
HIV-1 reverse transcriptase mutants resistant to nonnucleoside reverse transcriptase inhibitors do not adversely affect DNA synthesis: pre-steady-state and steady-state kinetic studies.
|
| |
J Acquir Immune Defic Syndr,
42,
405-411.
|
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T.Maruyama,
S.Kozai,
Y.Demizu,
M.Witvrouw,
C.Pannecouque,
J.Balzarini,
R.Snoecks,
G.Andrei,
and
E.De Clercq
(2006).
Synthesis and anti-HIV-1 and anti-HCMV activity of 1-substituted 3-(3,5-dimethylbenzyl)uracil derivatives.
|
| |
Chem Pharm Bull (Tokyo),
54,
325-333.
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|
T.S.Walter,
C.Meier,
R.Assenberg,
K.F.Au,
J.Ren,
A.Verma,
J.E.Nettleship,
R.J.Owens,
D.I.Stuart,
and
J.M.Grimes
(2006).
Lysine methylation as a routine rescue strategy for protein crystallization.
|
| |
Structure,
14,
1617-1622.
|
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|
|
|
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|
X.Wang,
Q.Lou,
Y.Guo,
Y.Xu,
Z.Zhang,
and
J.Liu
(2006).
The design and synthesis of 9-phenylcyclohepta[d]pyrimidine-2,4-dione derivatives as potent non-nucleoside inhibitors of HIV reverse transcriptase.
|
| |
Org Biomol Chem,
4,
3252-3258.
|
|
|
|
|
|
|
F.J.Blocker,
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L.H.Conlan,
L.Qi,
M.Belfort,
and
A.M.Lambowitz
(2005).
Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase.
|
| |
RNA,
11,
14-28.
|
|
|
|
|
|
|
G.F.Sun,
X.X.Chen,
F.E.Chen,
Y.P.Wang,
E.De Clercq,
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PDB code:
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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