Literature summary for 3.1.13.2 extracted from

Himmel, D.M.; Sarafianos, S.G.; Dharmasena, S.; Hossain, M.M.; McCoy-Simandle, K.; Ilina, T.; Clark, A.D.; Knight, J.L.; Julias, J.G.; Clark, P.K.; Krogh-Jespersen, K.; Levy, R.M.; Hughes, S.H.; Parniak, M.A.; Arnold, E.
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site (2006), ACS Chem. Biol., 1, 702-712.

Application

Application	Comment	Organism
drug development	the enzyme is a target for anti-HIV drug development	Human immunodeficiency virus 1

Crystallization (Commentary)

Crystallization (Comment)	Organism
enzyme bound to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide, by vapor diffusion in microseeded hanging drops containing equal volumes of protein and reservoir solution containing 50 mM imidazole, pH 6.4, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5% glucose, 11.5% PEG 8000 at 4°C, mixing 0.0074 ml of 20 mM inhibitor in DMSO with 0.0025 ml of 20% beta-octyl glucopyranoside, of this solution, 0.0075 ml is combined with 0.065 ml of 40 mg/ml RT and 0.0575 ml of additional RT buffer containing 10 mM Tris, pH 8.0, and 75 mM NaCl on ice, X-ray diffraction structure determination and anaylsis at 3.15 A resolution	Human immunodeficiency virus 1

Crystallization (Comment)

Organism

enzyme bound to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide, by vapor diffusion in microseeded hanging drops containing equal volumes of protein and reservoir solution containing 50 mM imidazole, pH 6.4, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5% glucose, 11.5% PEG 8000 at 4°C, mixing 0.0074 ml of 20 mM inhibitor in DMSO with 0.0025 ml of 20% beta-octyl glucopyranoside, of this solution, 0.0075 ml is combined with 0.065 ml of 40 mg/ml RT and 0.0575 ml of additional RT buffer containing 10 mM Tris, pH 8.0, and 75 mM NaCl on ice, X-ray diffraction structure determination and anaylsis at 3.15 A resolution

Human immunodeficiency virus 1

Protein Variants

Protein Variants	Comment	Organism
D67N/K70R/T215F/K219Q	the mutant shows reduced sensitivity to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide	Human immunodeficiency virus 1
V106A/Y181C	the mutant shows reduced sensitivity to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide	Human immunodeficiency virus 1
Y181C	the mutant shows reduced sensitivity to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide	Human immunodeficiency virus 1
Y188L	the mutant shows reduced sensitivity to inhibitor (E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide	Human immunodeficiency virus 1

Inhibitors

Inhibitors	Comment	Organism
(E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide	i.e. DHBNH, highly specific, noncompetitive, binding site analysis, the inhibitor binds near both the polymerase active site and the non-nucleoside reverse transcriptase inhibitor binding pocket, it specifically interacts with conserved residues Asp186 and Trp229 and has substantial interactions with the backbones of several less well-conserved residues, overview, substituted inhibitor derivatives, that interact with the nucleoside analog RT inhibitor-binding pocket, inhibit both the polymerase and RNH activities of reverse transcriptase, DHBNH interacts with other residues, including Val108, Leu187, Tyr188, Lys223, Phe227, and Leu228	Human immunodeficiency virus 1
4'-chloro-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide	-	Human immunodeficiency virus 1
4-(dimethylamino)-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide	-	Human immunodeficiency virus 1
4-methoxy-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide	-	Human immunodeficiency virus 1
4-tert-butyl-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide	-	Human immunodeficiency virus 1
additional information	inhibition mechanism, overview, antiviral activity and cytotoxic effects of inhibitors, overview	Human immunodeficiency virus 1
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-methylbenzohydrazide	-	Human immunodeficiency virus 1
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-phenoxybenzohydrazide	-	Human immunodeficiency virus 1
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide	-	Human immunodeficiency virus 1
N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide	-	Human immunodeficiency virus 1
N-(4-tert-butylbenzoyl)-2-hydroxy-1-naphthaldehyde hydrazone	i.e. BBNH, highly specific, a substituted inhibitor derivative, that interacts with the nucleoside analog RT inhibitor-binding pocket, and inhibits both the polymerase and RNH activities of reverse transcriptase	Human immunodeficiency virus 1
N-acyl hydrazone analogues	-	Human immunodeficiency virus 1

Metals/Ions

Metals/Ions	Comment	Organism	Structure
K+	-	Human immunodeficiency virus 1
Mg2+	-	Human immunodeficiency virus 1

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
DNA-RNA hybrid + H2O	Human immunodeficiency virus 1	-	DNA + RNA nucleotides	-	?

Organism

Organism	UniProt	Comment	Textmining
Human immunodeficiency virus 1	P03366	i.e. HIV-1	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
DNA-RNA hybrid + H2O	-	Human immunodeficiency virus 1	DNA + RNA nucleotides	-	?
DNA-RNA hybrid + H2O	-	Human immunodeficiency virus 1	DNA nucleotides + RNA nucleotides	-	?
additional information	the reverse transcriptase has two enzyme activities, one of which is the RNase H, enzyme-ligand interactions, overview	Human immunodeficiency virus 1	?	-	?

Subunits

Subunits	Comment	Organism
dimer	HIV-1 reverse transcriptase is a heterodimer consisting of a 66 kDa p66 subunit and a 51 kDa p51 subunit. The two polypeptide chains have 440 N-terminal amino acid residues in common, these comprise four polymerase subdomains: the thumb, palm, fingers, and connection, the C-terminus of p66 contains an additional 120 amino acid residues that form the bulk of the RNH domain	Human immunodeficiency virus 1

Synonyms

Synonyms	Comment	Organism
RNase H	-	Human immunodeficiency virus 1
RNH	-	Human immunodeficiency virus 1

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Human immunodeficiency virus 1

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Human immunodeficiency virus 1

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor
additional information	-	inhibition of mutant enzymes by DHBNH and antiviral activity, overview	Human immunodeficiency virus 1	additional information
0.0005	-	-	Human immunodeficiency virus 1	(E)-3,4-dihydroxy-N'-((2-methoxynaphthalen-1-yl)methylene)benzohydrazide
0.002	-	-	Human immunodeficiency virus 1	4-(dimethylamino)-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
0.003	-	-	Human immunodeficiency virus 1	4-tert-butyl-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
0.005	-	-	Human immunodeficiency virus 1	N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
0.007	-	-	Human immunodeficiency virus 1	N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-phenoxybenzohydrazide
0.0075	-	-	Human immunodeficiency virus 1	4'-chloro-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]biphenyl-4-carbohydrazide
0.012	-	-	Human immunodeficiency virus 1	4-methoxy-N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
0.015	-	-	Human immunodeficiency virus 1	N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]benzohydrazide
0.015	-	-	Human immunodeficiency virus 1	N'-[(1E)-(2-methoxynaphthalen-1-yl)methylidene]-4-methylbenzohydrazide