Structure and conformation of 3′-azido-3′-deoxythymidine (AZT), an inhibitor of the HIV (AIDS) virus

1987 ◽  
Vol 65 (9) ◽  
pp. 2135-2139 ◽  
Author(s):  
George I. Birnbaum ◽  
Jerzy Giziewicz ◽  
Eric J. Gabe ◽  
Tai-Shun Lin ◽  
William H. Prusoff
Keyword(s):  
Active Form ◽  
Three Dimensional ◽  
Direct Methods ◽  
High Energy ◽  
Biologically Active ◽  
Dimensional Structure ◽  
Human Immunodeficiency Virus Replication ◽  
Monoclinic Space Group ◽  
Sugar Ring ◽  
Immunodeficiency Syndrome

3′-Azido-3′-deoxythymidine (AZT), an inhibitor of HIV (human immunodeficiency virus) replication, was recently found to improve the condition of patients suffering from AIDS (acquired immunodeficiency syndrome) or ARC (AIDS-related complex). An X-ray analysis of AZT was undertaken in order to determine the three-dimensional structure of this thymidine analogue. The crystals belong to the monoclinic space group P21 and the cell dimensions are a = 5.6282(4), b = 12.0130(7), c = 17.5072(10) Å, β = 95.946(5)°. The structure was determined by direct methods and refined to R = 0.028 for 2029 observed reflections. Two crystallographically independent molecules were found in the asymmetric unit. One of them, molecule A, adopts a conformation which is fairly common in nucleosides, viz. a C2′ endo/C3′ exo pucker of the furanose ring and a glycosidic torsion angle χCN = 53.4°. However, the conformation of molecule B is highly unusual. The sugar ring pucker is C3′ exo/C4′ endo and χCN = 2.3°. This high-energy conformation may represent the biologically active form of AZT. Its determination may therefore assist in the design of other inhibitors of HIV.

Structure and conformation of the hydrochloride of pseudoisocytidine, an antileukemic C-nucleoside

1980 ◽  
Vol 58 (16) ◽  
pp. 1633-1638 ◽  
Author(s):  
George I. Birnabaum ◽  
Kyoichi A. Watanabe ◽  
Jack J. Fox
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Direct Methods ◽  
Dimensional Structure ◽  
Side Chain ◽  
Hydrogen Atoms ◽  
Triclinic Space Group ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Sugar Ring

The three-dimensional structure of pseudoisocytidine hydrochloride was determined by X-ray crystallography. The crystals belong to the triclinic space group P1 and the cell dimensions are a = 6.623(2), b = 8.053(2), c = 6.201(2) Å, α = 108.35(2), β = 101.36(2), γ = 93.54(2) °. Intensity data were measured with a diffractometer and the structure was solved by a combination of heavy-atom and direct methods. Least-squares refinement, which included hydrogen atoms, converged at R = 0.040. The conformation about the glycosyl bond is anti (χCC = 21.6°), the pucker of the furanose ring is C(1′)exo, and the conformation of the —CH2OH side chain is gauche–trans (t). An examination of bond lengths indicates that of the three main resonance forms of the isocytosine cation the fully conjugated one contributes more to the structure than the cross-conjugated one. Bond angles in the sugar ring reflect its rare conformation.

Structure and conformation of the anticodon nucleoside 5-methoxyuridine in the solid state and in solution

1983 ◽  
Vol 61 (10) ◽  
pp. 2299-2304 ◽  
Author(s):  
George I. Birnbaum ◽  
Wayne J. P. Blonski ◽  
Frank E. Hruska
Keyword(s):  
Solid State ◽  
Three Dimensional ◽  
Direct Methods ◽  
Pyrimidine Ring ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
Hydrogen Atoms ◽  
Cell Dimensions ◽  
Enol Tautomer

The three-dimensional structure of 5-methoxyuridine (mo5U) was determined with much higher precision than in a previous study (Hillen etal. J. Carbohydr. Nucleosides Nucleotides, 5, 23 (1978)). The crystals belong to the monoclinic space group P21 and the cell dimensions are a = 8.916(2), b = 14.372(2), c = 4.714(1) Å, β = 97.44(2)°. Intensity data were measured with a diffractometer and the structure was solved by direct methods. Least-squares refinement, which included all hydrogen atoms, converged at R = 0.031. The conformation about the glycosyl bond is anti (χCN = 23.1°), the pucker of the ribose ring is C(3′)endo, and the conformation of the —CH2OH side chain is gauche+. A comparison of the bond lengths N(3)—C(4) and C(4)—O(4) with those in uridine does not support the conclusion of Hillen etal. about a shift to the enol tautomer in mo5U. However, there are other changes in the geometry of the pyrimidine ring due to substitution at C(5). A conformational analysis, based on 1H and 13C nmr data, shows that the preferred conformation in solution is that observed in the solid state.

scholarly journals Synthesis and crystal structure of a new polymorph of potassium europium(III) bis(sulfate) monohydrate, KEu(SO4)2·H2O

2018 ◽  
Vol 74 (2) ◽  
pp. 242-245 ◽  
Author(s):  
Avijit Kumar Paul
Keyword(s):  
Crystal Structure ◽  
Topological Analysis ◽  
Structural Connectivity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
Hydrothermal Conditions ◽  
Metal Sulfate ◽  
Synthesis And Crystal Structure ◽  
Trigonal Prismatic

The mixed-metal sulfate, KEu(SO4)2·H2O, has been obtained as a new polymorph using hydrothermal conditions. The crystal structure is isotypic with NaCe(SO4)2·H2O and shows a three-dimensional connectivity of the tetrahedral sulfate units with EuIII and KI ions. Tricapped trigonal–prismatic EuO9 units and square-antiprismatic KO8 units link the SO4 tetrahedra, building the three-dimensional structure. Topological analysis reveals the existence of two nodes with 6- and 10-connected nets. The compound was previously reported [Kazmierczak & Höppe (2010). J. Solid State Chem. 183, 2087–2094] in the monoclinic space group P21/c with a similar structural connectivity and coordination environments to the present compound.

scholarly journals Crystallization and preliminary X-ray analysis of the major peanut allergen Ara h 1 core region

2010 ◽  
Vol 66 (9) ◽  
pp. 1071-1073 ◽  
Author(s):  
Cerrone Cabanos ◽  
Hiroyuki Urabe ◽  
Taro Masuda ◽  
Mary Rose Tandang-Silvas ◽  
Shigeru Utsumi ◽  
...  
Keyword(s):  
Sodium Citrate ◽  
Three Dimensional ◽  
Core Region ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Peg 400 ◽  
Ara H 1 ◽  
Peanut Allergens

Peanuts contain some of the most potent food allergens known to date. Ara h 1 is one of the three major peanut allergens. As a first step towards three-dimensional structure elucidation, recombinant Ara h 1 core region was cloned, expressed inEscherichia coliand purified to homogeneity. Crystals were obtained using 0.1 Msodium citrate pH 5.6, 0.1 MNaCl, 15% PEG 400 as precipitant. The crystals diffracted to 2.25 Å resolution using synchrotron radiation and belonged to the monoclinic space groupC2, with unit-cell parametersa= 156.521,b= 88.991,c= 158.971 Å, β = 107.144°. Data were collected at the BL-38B1 station of SPring-8 (Hyogo, Japan).

scholarly journals A helminth chitinase structurally similar to mammalian chitinase displays immunomodulatory properties

2019 ◽  
Author(s):  
Friederike Ebner ◽  
Katja Balster ◽  
Katharina Janek ◽  
Agathe Niewienda ◽  
Piotr H. Malecki ◽  
...  
Keyword(s):  
Inflammatory Marker ◽  
Disease Model ◽  
Three Dimensional ◽  
Gastrointestinal Nematode ◽  
Airway Hyperreactivity ◽  
Allergic Airway Disease ◽  
Biologically Active ◽  
Dimensional Structure ◽  
Trichuris Suis ◽  
Immunomodulatory Properties

AbstractPreviously, we reported significant immunomodulatory effects of the entire excretory-secretory (ES) proteins of the first larval stage (L1) of the gastrointestinal nematodeTrichuris suisin a rodent model of allergic hyperreactivity. In the present study, we aimed to identify the proteins accounting for the modulatory effects of theT. suisL1 ES proteins and thus studied selected components for their immunomodulatory efficacy in an OVA-induced allergic airway disease model. In particular, an enzymatically activeT. suischitinase mediated amelioration of airway hyperreactivity, primarily associated with suppression of eosinophil recruitment into the lung. The three-dimensional structure of theT. suischitinase as determined by high-resolution X-ray crystallography revealed significant similarities to mouse acidic mammalian chitinase (AMCase). In addition, the unique ability ofT. suischitinase to form dimers, as well as acidic surface patches within the dimerization region may contribute to the formation of cross-reactive antibodies to the mouse homologs. This hypothesis is supported by the observation thatT. suischitinase treatment induced cross-reactive antibodies to mouse AMCase and chitinase-like protein BRP-39 in the AHR model. In conclusion, a biologically activeT. suischitinase exhibits immunomodulatory properties despite its structural similarity to the mammalian counterpart.Author summaryExperimental immunotherapy via reintroduction of intestinal worms to treat and prevent autoimmune, chronic inflammatory or allergic diseases is being discussed but the underlying mechanisms are still not fully understood. Here, we investigated the immunomodulatory potential of specific proteins of the whipwormTrichuris suisthat are secreted very early during larval development. Using a murine model of allergic lung disease, we show that in particular oneT. suisprotein, functionally characterized as an active chitinase, is reducing the lung inflammation. TheT. suischitinases three-dimensional protein structure revealed remarkable similarities to the hosts’ chitinase, an enzyme known to play a pivotal role in lung allergy. We also show that treatment with the helminth chitinase induced cross-reactive antibody responses against murine chitinase and chitinase-like proteins, both being inflammatory marker and regulators of type 2 immunity. Thus, our study provides a novel mechanism of immunomodulation by helminth components and may contribute to a better understanding of clinical responses of patients receiving helminthic therapy.

Hydrothermal Synthesis and Structure of Neptunium(V) Oxide

2006 ◽  
Vol 985 ◽  
Author(s):  
Tori Z. Forbes ◽  
Peter C. Burns ◽  
L. Soderholm ◽  
S. Skanthakumar
Keyword(s):  
Hydrothermal Synthesis ◽  
Low Temperature ◽  
Single Crystals ◽  
Hydrothermal Reaction ◽  
Three Dimensional ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Unique Data ◽  
Ccd Detector

AbstractSingle crystals of Np2O5 have been synthesized by low-temperature hydrothermal reaction of a Np5+ stock solution with natural calcite crystals. The structure of Np2O5 was solved by direct methods and refined on the basis of F2 for all unique data collected on a Bruker X-ray diffractometer equipped with an APEX II CCD detector. Np2O5 is monoclinic, space group P2/c, with a = 8.168(2) Å, b = 6.584(1) Å, c = 9.3130(2) Å, β = 116.01(1)˚, V = 449.8(2) Å3, and Z = 1. The structure contains chains of edge-sharing neptunyl pentagonal bipyramids linked into sheets through cation-cation interactions with distorted neptunyl square bipyramids. Additional cation-cation interactions connect the sheets into a three-dimensional framework. The formation of Np2O5 on the surface of calcite crystals has important implications for the precipitation of isolated neptunyl phases in natural aqueous systems.

scholarly journals Crystal structure and thermal behaviour of pyridinium styphnate

2015 ◽  
Vol 71 (2) ◽  
pp. 117-120 ◽  
Author(s):  
Selvarasu Muthulakshmi ◽  
Doraisamyraja Kalaivani
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Nitro Group ◽  
Benzene Ring ◽  
Three Dimensional ◽  
High Energy ◽  
High Energy Density ◽  
Dimensional Structure ◽  
Molecular Salt ◽  
Ring Motif

In the crystal structure of the title molecular salt, C5H6N+·C6H2N3O8−(systematic name: pyridinium 3-hydroxy-2,4,6-trinitrophenolate), the pyridinium cation and the 3-hydroxy-2,4,6-trinitrophenolate anion are linked through bifurcated N—H...(O,O) hydrogen bonds, forming anR12(6) ring motif. The nitro groupparawith respect to phenolate ion forms an intramolecular hydrogen bond with the adjacent phenolic –OH group, which results in anS(6) ring motif. The nitro group flanked by the phenolate ion and the phenolic –OH group deviates noticeably from the benzene ring, subtending a dihedral angle of 89.2 (4)°. The other two nitro groups deviate only slightly from the plane of the benzene ring, making dihedral angles of 2.8 (4) and 3.4 (3)°. In the crystal, the 3-hydroxy-2,4,6-trinitrophenolate anions are linked through O—H...O hydrogen bonds, forming chains along [100]. These anionic chains, to which the cations are attached, are linkedviaC—H...O hydrogen bonds, forming a three-dimensional structure. Impact friction sensitivity tests and TGA/DTA studies on the title molecular salt imply that it is an insensitive high-energy-density material.

Crystal and molecular structure of Bis(4-amino-3,5,6-trichloropicolinato)-manganese(II) dihydrate

1981 ◽  
Vol 34 (4) ◽  
pp. 891 ◽  
Author(s):  
G Smith ◽  
EJ O'Reilly ◽  
CHL Kennard
Keyword(s):  
Molecular Structure ◽  
Crystal And Molecular Structure ◽  
Three Dimensional ◽  
Direct Methods ◽  
Polymer Chains ◽  
Monoclinic Space Group ◽  
Carboxylate Oxygen ◽  
Group 12 ◽  
Distorted Octahedral ◽  
A Cell

The manganese(II) complex [Mn(picl)2,2H2O]n of the herbicide picloram has been prepared and the crystal and molecular structure determined from three-dimensional X-ray data collected by counter methods. The crystals of the complex are monoclinic, space group 12/a with two complex units in a cell of dimensions a 23·052(5), b 13·840(2), c 6·441(1) �, β 98·20(1)�. The structure was solved by direct methods and refined by full matrix least squares to unweighted and weighted Rfactors of 0·035 and 0·038 respectively for 887 'observed' reflections. The polymer is best described as having a centrosymmetric two-molecule unit [Mn-O, 2·162(3), 2·246(3) �] with two oxo bridges between manganese centres through two single carboxylate oxygens of the four substituted picolinate ligands. The two molecules are related by a twofold axis. The units form infinite one-dimensional polymer chains in the c direction through oxo bridges involving one oxygen from the other two picolinate ligands [Mn-Mn 3·636(1)�]. The bis(bidentate)picolinate bites are completed by the pyridlne nitrogens [Mn-N, 2·313(4) �] giving a very distorted octahedral MnO4N2 coordination sphere about each manganese [N-Mn-N', 97.0(3)�; O-Mn-O range, 68·9-168.2(3)�; O-Mn-Nrange, 69·9-138·5(3)�]. The lattice waters are involved in hydrogen-bonding interactions which link the polymer in the a crystallographic direction with the uncoordinated carboxylate oxygen ( O···O,2·824, 2·936 �) and the 4-amino groups from the adjacent picolinate ligand (N· ··0, 2·852, 3·030�).

Thyroid Hormone Stereochemistry. II. Molecular Structure of Thyronine HCl Ethyl Ester Monohydrate

1974 ◽  
Vol 52 (17) ◽  
pp. 3042-3047 ◽  
Author(s):  
Arthur Camerman ◽  
Norman Camerman
Keyword(s):  
Ethyl Ester ◽  
Three Dimensional ◽  
Chloride Ion ◽  
Dimensional Structure ◽  
Side Chain ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Ether Linkage ◽  
Cell Dimensions ◽  
Phenyl Rings

The three-dimensional structure of L-thyronine, the non-iodinated physiologically inactive analog of thyroxine, has been determined by single crystal X-ray diffraction and compared to the active thyroid hormones. The compound crystallized as the monohydrate of thyronine hydrochloride ethyl ester in the monoclinic space group P21 with cell dimensions a = 10.502, b = 5.165, c = 17.940 Å, β = 109.74°. The structure was solved by Patterson methods to find the chloride ion and iterative Fourier maps to locate the rest of the atoms. Refinement was by anisotropic full-matrix least squares to convergence at R = 0.048.The two phenyl rings adopt a twisted orientation with respect to each other with angles of −37° and −67° between the plane of the inter-ring ether linkage and the planes of the α- and β-rings, respectively. This orientation differs considerably from that found in the iodinated thyronines. The conformation of the alanine side chain is remarkably similar to that of the alanine in the iodinated thyronines.

scholarly journals Crystal structures ofN2,N3,N5,N6-tetrakis(pyridin-2-ylmethyl)pyrazine-2,3,5,6-tetracarboxamide andN2,N3,N5,N6-tetrakis(pyridin-4-ylmethyl)pyrazine-2,3,5,6-tetracarboxamide

2017 ◽  
Vol 73 (2) ◽  
pp. 300-305
Author(s):  
Dilovan S. Cati ◽  
Helen Stoeckli-Evans
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Monoclinic Space Group ◽  
Compound I ◽  
Acta Cryst ◽  
Pyrazine Ring ◽  
Bond Forming ◽  
Compound Ii

The title compounds, C32H28N10O4· unknown solvent, (I), and C32H28N10O4, (II), are pyrazine-2,3,5,6-tetracarboxamide derivatives. In (I), the substituents are (pyridin-2-ylmethyl)carboxamide, while in (II), the substituents are (pyridin-4-ylmethyl)carboxamide. Both compounds crystallize in the monoclinic space groupP21/n, withZ′ = 1 for (I), andZ′ = 0.5 for (II). The whole molecule of (II) is generated by inversion symmetry, the pyrazine ring being situated about a center of inversion. In (I), the four pyridine rings are inclined to the pyrazine ring by 83.9 (2), 82.16 (18), 82.73 (19) and 17.65 (19)°. This last dihedral angle involves a pyridine ring that is linked to the adjacent carboxamide O atom by an intramolecular C—H...O hydrogen bond. In compound (II), the unique pyridine rings are inclined to the pyrazine ring by 33.3 (3) and 81.71 (10)°. There are two symmetrical intramolecular C—H...O hydrogen bonds present in (II). In the crystal of (I), molecules are linked by N—H...O and N—H...N hydrogen bonds, forming layers parallel to (10-1). The layers are linked by C—H...O and C—H...N hydrogen bonds, forming a three-dimensional framework. In the crystal of (II), molecules are linked by N—H...N hydrogen bonds, forming chains propagating along the [010] direction. The chains are linked by a weaker N—H...N hydrogen bond, forming layers parallel to the (101) plane, which are in turn linked by C—H...O hydrogen bonds, forming a three-dimensional structure. In the crystal of compound (I), a region of disordered electron density was treated with the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst. C71, 9–18]. Their contribution was not taken into account during refinement. In compound (II), one of the pyridine rings is positionally disordered, and the refined occupancy ratio for the disordered Car—Car—Npyatoms is 0.58 (3):0.42 (3).

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