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Y In

Publications and source records attributed to Y In.

33 records · Page 2Linked to original sources
PubMed1992

Conformational feature of neuroactive domoic acid: X-ray structural comparison with isodomoic acid A and alpha-kainic acid.

As an aid for developing a new type of potent insecticide acting on the neuromuscular junction, conformational characteristics of domoic acid and isodomoic acid A, the naturally occurring glutamate agonists, were investigated by X-ray crystal analyses. Conformational comparison with a neuroactive alpha-kainic acid provides information concerning the stereochemical feature responsible for the biological activity.

Insecticides↗
PubMed1992

Effect of the D-Phe2 residue on molecular conformation of an endogenous neuropeptide achatin-I. Comparison of X-ray crystal structures of achatin-I (H-Gly-D-Phe-Ala-Asp-OH) and achatin-II (H-Gly-Phe-Ala-Asp-OH).

The molecular conformation of achatin-II neutral form (H-Gly-Phe-Ala-Asp-OH), an endogenous peptide from the Achatina fulica ganglia, was elucidated by X-ray crystal analysis. The molecule takes an extended beta-pleated structure stabilized by 5 intermolecular hydrogen bonds with the antiparallely arranged molecules. This is in contrast with the turn conformation of a neuroactive achatin-I (H-Gly-D-Phe-Ala-Asp-OH) [(1992) FEBS Lett. 276,95-97]. The conformational comparison of both of the molecules makes clear the structural role which D-Phe residue of achatin-I plays in forming a definite active form.

Amino Acid Sequence↗
PubMed1992

Molecular conformation of ascidiacyclamide, a cytotoxic cyclic peptide from Ascidian: X-ray analyses of its free form and solvate crystals.

In order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x-ray diffraction method. Crystal I showed a pseudo C2-symmetric saddle-shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2-symmetric molecules (named Mol-A and -B) per asymmetric unit. Mol-A and -B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar-ring N atoms and nonpolar D-Val side-chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x-ray results.

Animals↗
PubMed1992

Crystal structure and molecular conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide containing a D-amino acid residue.

In order to investigate the active conformation of achatin-I (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide from the Achatina fulica ganglia, its crystal structure and molecular conformation were analysed by the X-ray diffraction method. Crystals from methanol/dioxane are monoclinic, space group P2(1) with a = 5.083(1), b = 9.125(1), c = 20.939(3) A, beta = 94.73(1) degrees. The structure was solved by direct methods and refined to R = 0.051 for 1714 independent reflections with /Fo/ greater than sigma (Fo). The molecule exists as a zwitterion with the Gly N-terminal end protonated and Asp beta-carboxyl deprotonated; the C-terminal of Asp is in a neutral state. The molecule takes a kind of beta turn structure with the D-Phe-Ala residues at the corner of the bend. This turn conformation is primarily formed by the strong intramolecular hydrogen bonds of NH(Gly)...O delta 1 (Asp) and NH(Asp)...O delta 1 (Asp) pairs, thus forming a 15-membered ring structure. Judging from the published data concerning the structure-activity relationship, this turn conformation may reflect an important feature related to the neuroexcitatory activity of achatin-I.

Amino Acid Sequence↗
PubMed1992

Calcium binding to phospholipid: structural study of calcium glycerophosphate.

To consider possible interaction of the phospholipid membrane with calcium ions, crystal structures of calcium dl-alpha- and beta-glycerophosphates (alpha- and beta-CaGs, respectively) were investigated by X-ray diffraction methods. After many attempts, relatively large single crystals of beta-CaG were prepared from the aqueous solution containing HCl, while crystals of CaHPO4.2H2O were obtained from alpha-CaG solution under the same crystallization conditions. The crystal structure of beta-CaG is orthorhombic with space group Pna2(1) and cell dimensions of a = 8.251(1), b = 13.038(3), c = 25.483 (10) A, V = 2741.5 (13) A3 and Z = 16 [four molecules (A to D) in an asymmetric unit]. Molecules of A to D took, as a whole, similar extended conformations, although A and B were different from C and D in the orientation about a glycerol C-C bond. Four independent beta-glycerophosphates commonly act as two types of bidentate ligands, where one is the coordination to the calcium ion by the glycerol O(1) and phosphate O(22) atoms, and the other by the phosphate O(22) and O(23) atoms, thus forming the calcium coordination of a distorted square plane, respectively. Each of four independent calcium ions forms the same coordination geometry of a distorted pentagonal bipyramid. Infinite double layers consisting of alternate A/B molecules and of alternative C/D ones and sandwiching calcium ions were arranged face-to-face along the b-direction and were piled up in the a-direction, thus forming the stacked bilayer unit with the thickness of d002 = 12.75 A. The elaborate networks of calcium coordinations and hydrogen bondings were formed among the layers and stabilized the crystal structure. Based on the structural parameters of the present beta-CaG crystal, a possible interaction model of phospholipid with calcium ions was proposed.

Calcium↗
PubMed1991

X-ray crystallographic conformational study of 5'-O-[N-(L-alanyl)-sulfamoyl]adenosine, a substrate analogue for alanyl-tRNA synthetase.

In order to elucidate the substrate specificity of alanyl-tRNA synthetase, 5'-O-[N-(L-alanyl)sulfamoyl]adenosine (Ala-SA), an analogue of alanyl-AMP, was chemically synthesized. Its binding ability is similar to that of the substrate based on the inhibitory activity for the aminoacylation of alanyl-tRNA synthetase. Taking advantage of the stable sulfamoyl bond of Ala-Sa, compared with the highly labile aminoacyl bond of alanyl-AMP, the molecular conformation of the former inhibitor was studied by X-ray single crystal analysis. Crystal data are as follows: C13H19N7O7S.2H2O, space group C2, a = 39.620(6), b = 5.757(1), c = 20.040(3) A, beta = 117.2(1) degrees, V = 4065(9) A3, Z = 8, and final R = 0.065 for 2785 independent reflections of F(2)0 greater than or equal to 2 sigma (F0)2. In the crystal, the molecule is in a zwitterionic state with the terminal amino group protonated and sulfamoyl group deprotonated, and takes an open conformation, where the L-alanine moiety is located far from the adenosine moiety with gauche/trans and trans orientations about the exocyclic C(4')-C(5') and C(5')-O(5') bonds, respectively. The conformation of the adenosine moiety is anti for the glycosyl bond and C(3')-endo for the ribose puckering, and alanine is in the usually observed trans region for the psi torsion angle. The molecular dimensions of the sulfamoyl group are nearly the same as those of the phosphate group. The biological significance of the observed Ala-SA conformation is discussed in relation with the molecular conformation of tyrosyl-AMP complexed with tyrosyl-tRNA synthetase.

Adenosine↗
PubMed1991

Structural study of aldose reductase inhibitors. Ten oxazolecarbamate derivatives.

(1) Benzyl 4-isopropyl-5-phenyl-2-oxazolecarbamate, C20H20N2O3, Mr = 336.39, P1, a = 19.469 (7), b = 11.270 (3), c = 8.667 (3) A, alpha = 95.48 (3), beta = 99.61 (3), gamma = 104.96 (3) degrees, V = 1792 (1) A3, Z = 4, Dm = 1.266 (2), Dx = 1.247 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.49 cm-1, F(000) = 712, T = 288 K, R = 0.048 for 5244 reflections. (2) Benzyl 4-ethyl-5-phenyl-2-oxazolecarbamate, C19H18N2O3, Mr = 322.37, P2(1)/n, a = 9.131 (7), b = 18.81 (1), c = 9.680 (8) A, beta = 101.07 (3) degrees, V = 1631 (2) A3, Z = 4, Dm = 1.310 (2), Dx = 1.313 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.92 cm-1, F(000) = 680, T = 288 K, R = 0.063 for 2535 reflections. (3) Benzyl 4-methyl-5-phenyl-2-oxazolecarbamate, C18H16N2O3, Mr = 308.34, P2(1)/n, a = 9.210 (7), b = 8.785 (6), c = 19.800 (9) A, beta = 99.60 (3) degrees, V = 1580 (2) A3, Z = 4, Dm = 1.299 (3), Dx = 1.300 g cm-3, lambda (Cu K alpha) = 1.5418 A, mu = 6.93 cm-1, F(000) = 648, T = 288 K, R = 0.057 for 2190 reflections.(ABSTRACT TRUNCATED AT 250 WORDS)

Aldehyde Reductase↗
PubMed1991

Molecular and crystal structures of 2-(2-pyridyl)thioacetamide derivatives and possible relationship with inhibitory activity for gastric acid secretion.

As a possible method to determine the key atoms and their spatial orientation which are necessary for the gastric mucosal protective and antisecretory activity, crystal structures of sixteen 2-(2-pyridyl) thioacetamide derivatives have been analyzed by the X-ray diffraction method. The characteristics of the molecular and crystal structures of the derivatives are described in this paper. The energetic stability of the molecular conformation is also investigated by means of the molecular force field method. Using the conformational data, a possible relationship between the stereostructure and inhibitory activity for gastric acid secretion is considered by QSAR analyses. The results suggest that the activity is related to the overall molecular conformation, and that the spatial distribution of the side-chain polar atoms with respect to the fixed pyridine is especially important for the activity.

Animals↗
PubMed1990

Molecular conformation of achatin-I, an endogenous neuropeptide containing D-amino acid residue. X-ray crystal structure of its neutral form.

The molecular conformation of achatin-I neutral form (H-Gly-D-Phe-Ala-Asp-OH), an endogenous neuropeptide, was elucidated by X-ray crystal analysis. The molecule has a type II' beta-turn structure with the D-Phe-Ala residues at the corner of the bend, which is further stabilized by two NH(Gly)...C gamma = O sigma(Asp) and NH(Asp)...C gamma = O sigma(Asp) intramolecular hydrogen bonds. This turn conformation may be an important feature of achatin-I related to its neuroexcitatory activity.

Amino Acid Sequence↗
PubMed1990

Molecular conformations of aminophenylimidazoles exhibiting antiulcer activities.

To experimentally clarify a possible stereostructure-activity relationship proposed for H2-receptor antagonists, three 5-aminophenylimidazoles (1, 2 and 3), in which respective amino groups are located on the ortho, meta and para positions of the benzene ring, were synthesized and examined for their conformational characteristics using X-ray diffraction and proton nuclear magnetic resonance (1H-NMR) methods, and for antiulcer activities on rats and H2-receptor antagonist activities in guinea pig. The ortho isomer 1, which preferentially formed an intramolecular N-H (amino)...N (imidazole) hydrogen bond, showed the highest antiulcer activity with half the efficacy of cimetidine. On the other hand, none of 1, 2 and 3 showed significant H2-receptor antagonist activity. Based on these results, the conformational characteristic for the exhibition of antiulcer activity has been discussed.

Aniline Compounds↗
PubMed1989

Structure of 5-methoxy-2-([4-methoxy-3,5-dimethyl-2-pyridinyl) methyl]sulfinyl)-1H-benzimidazole (omeprazole).

C17H19N3O3S, Mr = 345.42, triclinic, P1, a = 10.686 (5), b = 10.608 (7), c = 9.666 (6) A, alpha = 119.75 (5), beta = 112.02 (5), gamma = 68.33 (4) degrees, V = 859 (1) A3, Z = 2, Dm = 1.332 (2), Dx = 1.335 g cm-3, Cu K alpha, lambda = 1.5418 A, mu = 18.04 cm-1, F(000) = 364, T = 293 K, R = 0.057 for 1962 observed reflections. The methylsulfinyl group, which adopts a trans conformation, links the pyridine and benzimidazole rings in an almost coplanar orientation. Thus the molecule, as a whole, adopts a nearly extended form. Two centrosymmetrically related molecules form a cyclic dimer by intermolecular N-H...O hydrogen bonding, and the dimers are held together by van der Waals contacts between the neighboring aromatic rings in the crystal structure.

Omeprazole↗
PubMed1989

Structural study of histamine H2-receptor antagonists. Five 3-[2-(diamino-methyleneamino)-4-thiazolylmethylthio]propionamidine and -amide derivatives.

(1) N2-Cyano-3-[2-(diaminomethyleneamino)-4- thiazolylmethylthio]propionamidine monohydrate, C9H13N7S2.H2O, Mr = 301.39, P1, a = 11.089 (4), b = 9.130 (6), c = 7.033 (5) A, alpha = 100.99 (6), beta = 83.86 (5), gamma = 86.80 (7) degrees, V = 692.9 (6) A3, Z = 2, Dm = 1.443 (2), Dx = 1.444 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 34.86 cm-1, F(000) = 316, T = 293 K, R = 0.043 for 2219 reflections. (2) 3-[2-Diaminomethyleneamino)-4- thiazolylmethylthio]-N2-sulfamoylpropionamidine (famotidine) hydrochloride, C8H15N7O2S3.HCl, Mr = 373.90, Cc, a = 15.205 (3), b = 14.442 (3), c = 9.262 (1) A, beta = 124.00 (5) degrees, V = 1686.1 (7) A3, Z = 4, Dm = 1.470 (2), Dx = 1.473 g cm-3, mu(Cu K alpha) = 56.09 cm-1, F(000) = 776, T = 293 K, R = 0.036 for 1411 reflections. (3) 3-[2-(Diaminomethyleneamino)-4-thiazolylmethylthio]-propi ona mide, C8H13N5OS2, Mr = 259.35, P2(1)2(1)2(1), a = 5.472 (1), b = 18.260 (5), c = 11.890 (3) A, V = 1188.0 (5) A3, Z = 4, Dm = 1.448 (1), Dx = 1.450 g cm-3, mu(Cu K alpha) = 39.26 cm-1, F(000) = 544, T = 293 K, R = 0.036 for 1260 reflections.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗
PubMed1988

Structure-activity relationship of aldose reductase inhibitors based on X-ray crystal structures of oxazolecarbamate derivatives.

In order to elucidate the key atoms and/or stereostructures necessary for the inhibitory emergence of aldose reductase, crystal structure determinations were carried out for 11 oxazolecarbamate analogues, which have similar chemical and physicochemical properties but different inhibitory activities. The molecular conformations, revealed by X-ray analyses, were also ascertained to be energetically stable from theoretical conformational energy calculations. A surprising degree of conformational similarity was observed for the potent inhibitors. The analyses of the quantitative structure--activity relationships showed that the molecular conformation and the dipole moment, as well as the hydrophobicity at the oxazole C5-site, were important for high activity.

Aldehyde Reductase↗
PubMed1987

On the structure-activity relationship of histamine H2-receptor antagonists based on the X-ray crystal structures and 1H-NMR spectra of amidine derivatives.

The conformation of six amidine compounds, which possess a common 3-[(4-thiazolyl)methylthio]propionylamidine framework but exhibit different activities as histamine H2-receptor antagonists, have been subjected to both single crystal X-ray structural and 1H-NMR analyses. The X-ray studies suggest a correlation between antagonist activity and the relative spatial orientation of the thiazolyl and amidine nitrogen atoms. This correlation is supported by a comparison of the conformations observed for the amidines with those of other H2-receptor antagonists and reveal that a folded conformation, specifically the NH...N intramolecular hydrogen-bonded configuration, is important for antagonist activity. The 1H-NMR measurements on the active amidine compounds show that the intramolecular NH...N bond is likely to be present in solution.

Amidines↗