Structure and conformation of 5-methoxymethyl-2′-deoxycytidine

1990 ◽  
Vol 68 (6) ◽  
pp. 836-841 ◽  
Author(s):  
Zongchao Jia ◽  
Guy Tourigny ◽  
Louis T. J. Delbaere ◽  
Allan L. Stuart ◽  
Sagar V. Gupta
Keyword(s):  
Three Dimensional ◽  
Antiviral Agent ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
Side Chain ◽  
X Ray ◽  
Envelope Conformation ◽  
Anti Conformation ◽  
Sugar Ring ◽  
Antiherpes Activity

The three-dimensional structure of the antiviral agent 5-methoxymethyl-2′-deoxycytidine (MMdCyd) was deduced by X-ray crystallographic analysis. MMdCyd crystallized in space group P21 with a = 7.9255(6) Å; b = 16.1505(15) Å, c = 10.1861(5) Å, β = 103.801(5)°, and Z = 4 (2 molecules per asymmetric unit); R = 0.044 (Rw = 0.046) for 2560 observed reflections with net I > 3σ(I). The furanose ring adopts the C(3′)-exo envelope conformation (3E) in molecule A and the C(2′)-endo envelope conformation (2E) in molecule B. In the sugar ring of both crystallographically independent molecules A and B, the side chain at C(5′) has the g+ conformation. This appears to be a preferred geometry required for antiherpes activity in 2′-deoxyribonucleosides. The glycosyl linkage is anti with χ = 213.7° for the A molecule and 222.2° for the B molecule. With respect to this anti conformation, the methoxy group at C(5) in molecules A and B exhibits different conformations; it is on the same side of the pyrimidine plane as the deoxyribofuranose ring oxygen (O4′) in molecule B and on the opposite side in molecule A. Keywords: antiherpes agent, conformation, 5-methoxymethyl-2′-deoxycytidine, crystal structure.

Structure and conformation of 5-methoxymethyl-1-(2′-deoxy-β-D-lyxofuranosyl)uracil

1986 ◽  
Vol 64 (7) ◽  
pp. 1305-1309 ◽  
Author(s):  
J. Wilson Quail ◽  
Irena Ekiel ◽  
Ossama A. L. El-Kabbani ◽  
Guy Tourigny ◽  
Louis T. J. Delbaere ◽  
...  
Keyword(s):  
Crystallographic Analysis ◽  
Side Chain ◽  
Nmr Analysis ◽  
Space Group ◽  
X Ray ◽  
Envelope Conformation ◽  
Sugar Ring ◽  
Glycosidic Conformation

The structure of the nucleoside 5-methoxymethyl-1-(2′-deoxy-β-D-lyxofuranosyl)uracil (MMdLU) was deduced by X-ray crystallographic analysis. MMdLU crystallized in space group P21 with a = 8.719(4), b = 13.188(3), c = 5.701(3) Å, β = 109.56(2)° and Z = 2; R = 0.040 for 1208 unique reflections with net I > 2σ(I). The furanose ring adopts the rare C(4′)—exo envelope conformation (4E). The glycosyl linkage is anti (χ = 243.5°) and the C(5′) side chain has the t conformation. The conformation was also determined in solution by nmr analysis. The sugar ring exists in the N-conformation (97 ± 5%), the populations of the three rotamers about the exocyclic C(4′)—C(5′) bond were estimated to be g+:t:g− = 23%:59%:18% and the glycosidic conformation is predominantly anti.

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.

The crystal and molecular structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil. A very short C≡C triple bond

1984 ◽  
Vol 62 (1) ◽  
pp. 147-152 ◽  
Author(s):  
Mlroslaw Cygler ◽  
Wayne F. Anderson ◽  
Jerzy Giziewicz ◽  
Morris J. Robins
Keyword(s):  
Triple Bond ◽  
Crystal And Molecular Structure ◽  
Direct Methods ◽  
Pyrimidine Ring ◽  
Side Chain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Anti Conformation ◽  
Sugar Ring ◽  
Glycosidic Torsion Angle

The crystal structure of 5-(propyn-1-yl)-1-(β-D-arabinofuranosyl)uracil, an analog of the active antiherpes nucleoside 1-(β-D-arabinofuranosyl)thymine, was determined by X-ray diffraction. The compound crystallizes in the space group P212121 with a = 4.925(1), b = 14.326(2), c = 17.454 Å. Reflections were measured on a diffractometer and the structure was solved by direct methods. Least-squares refinement converged at R = 0.032 for 1159 observed reflections. The sugar ring exhibits an 3E or a C(3′)endo conformation with a pseudorotation angle P = 28.3° and puckering amplitude τm = 31.7°. The orientation of the —CH2OH side chain is g+. The base is in an anti conformation with respect to the sugar ring, with a glycosidic torsion angle χ = 33.7°. Changes in the C(5)—C(6) and C(6)—N(1) bond lengths suggest some interaction of the propynyl group with the pyrimidine ring. The C≡C bond length of 1.121 Å is very short. Its shortening could result from intermolecular interactions with the neighboring pyrimidine ring and nearby oxygen atoms.

scholarly journals Synthesis, spectroscopic and X-ray crystallographic analysis of N-(2-(2-(4-chlorophenoxy)acetamido)phenyl)-1H-indole-2-carboxamide

2019 ◽  
Vol 10 (3) ◽  
pp. 234-238
Author(s):  
Fares Hezam Al-Ostoot ◽  
Jigmat Stondus ◽  
Sumati Anthal ◽  
Geetha Doddenahally Venkatesh ◽  
Yasser Hussein Eissa Mohammed ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Direct Methods ◽  
Functional Materials ◽  
Crystallographic Analysis ◽  
Least Square ◽  
Dimensional Structure ◽  
Spectroscopic Techniques ◽  
Monoclinic Crystal ◽  
X Ray ◽  
Anti Oxidant

Medicinal chemistry of indole analogs constitutes important therapeutic agents with anti-oxidant, anti-HIV and anti-cancer activities. Indole nucleus is frequently found in synthetic and natural products, pharmaceuticals, functional materials, agrochemicals, etc. The title compound, N-(2-(2-(4-chlorophenoxy)acetamido)phenyl)-1H-indole-2-carboxamide (5), has been synthesized in good yield by stirring the compound N-(2-aminophenyl)-2-(4-chlorophenoxy)acetamide (3) with 1H-indole-2-carboxylic acid (4), in dry dichloromethane followed by the addition of 2,6-lutidine, and o-(benzotriazol-1-yl)-N,N,N',N'-tetramethyl uraniumtetrafluoroborate in cooled condition. Compound 5 was synthesized and characterized by the conventional spectroscopic techniques (1H NMR, 13C NMR and LC-MS) and the three-dimensional structure was elucidated by using single crystal X-ray diffraction methods. It crystallizes in the monoclinic crystal system with space group P21/c. The structure was solved by direct methods and refined by full matrix least square procedure to a final R value of 0.043 for 2490 observed reflections. Three intra-molecular interactions of the type N-H···N and C-H···N were observed. The packing of molecules in the unit cell is governed by N-H···O and C-H···O intermolecular H-boned interactions which leads to the formation of infinite staking chain along [001] direction. In addition, two weak C-H···π interactions also contribute to molecular packing.

scholarly journals Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach

2012 ◽  
Vol 68 (2) ◽  
pp. 175-177 ◽  
Author(s):  
V. P. Martini ◽  
A. Glogauer ◽  
J. Iulek ◽  
E. M. Souza ◽  
F. O. Pedrosa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Three Dimensional ◽  
Sodium Formate ◽  
Crystallographic Analysis ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Sequence Identity

LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase fromPseudomonas aeruginosaPAO1. Recombinant N-terminally His6-tagged LipC12 protein was expressed inEscherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 Msodium formate and 0.1 Mbis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space groupP4122, with unit-cell parametersa=b= 58.62,c = 192.60 Å.

scholarly journals Absolute Configuration of the Antiviral Agent (−)-cis-5-Fluoro-1-[2-Hydroxymethyl)-1,3-Oxathiolan-5-yl]Cytosine

1993 ◽  
Vol 4 (6) ◽  
pp. 369-375 ◽  
Author(s):  
P. van Roey ◽  
W. A. Pangborn ◽  
R. F. Schinazi ◽  
G. Painter ◽  
D. C. Liotta
Keyword(s):  
Absolute Configuration ◽  
Antiviral Agent ◽  
Crystallographic Analysis ◽  
Asymmetric Unit ◽  
Sulphur Atom ◽  
X Ray ◽  
Pyrimidine Nucleosides ◽  
Anti Conformation ◽  
Antiviral Nucleosides ◽  
Active Site Conformation

The structure and absolute configuration of (−)- cis-5-fluoro-1-[2-(hydroxymethyl)-1,3-oxathiolan-5-yl]cytosine (FTC), has been determined by X-ray crystallographic analysis. The results confirm that the L-isomer of the nucleoside analogue is the most active enantiomer and that the correct absolute configuration of (−)-FTC is 5-fluoro-(2′R,5′S)-(−)-1-[2-hydroxymethyl)oxathiolan-5-yl]-fluorocytosine. The two molecules in the asymmetric unit show conformations that combine conformational features of two other classes of potent antiviral nucleosides. Both oxathiolane rings have the 3′-sulphur atom in nearly perfect S3′- exo envelope conformations, similar to what is observed for 3′-azido-3′-deoxythymidine (AZT) and 2′,3′-dideoxycytidine. One of the two molecules has a glycosylic link conformation in which the base is eclipsed with the C5′-O1′ bond. This mimics the high- anti conformation that has been observed in the structures of several 2′,3′-didehydro-2′,3′-dideoxypyrimidine nucleosides but is inaccessible for saturated pyrimidine nucleosides. However, the observed conformations cannot be superimposed adequately with other active antiviral nucleosides to suggest a common ‘active site’ conformation.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

The three-dimensional structure of interleukin-1β

1988 ◽  
Vol 16 (6) ◽  
pp. 949-953 ◽  
Author(s):  
JOHN P. PRIESTLE ◽  
HANS-PETER SCHÄR ◽  
MARKUS G. GRÜTTER
Keyword(s):  
Polypeptide Chain ◽  
Three Dimensional ◽  
Interleukin 1Β ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
R Factor ◽  
The Core ◽  
Internal Sequence ◽  
Network Of Hydrogen Bonds

Summary The three-dimensional structure of human recombinant interleukin-1β has been determined at 0.24 nm resolution by X-ray crystallographic techniques. The partially refined model has a crystallographic R-factor of just under 19%. The structure is composed of 12 β-strands forming a complex network of hydrogen bonds. The core of the structure can best be described as a tetrahedron whose edges are each formed by two antiparallel β-strands. The interior of this structure is filled with hydrophobic side-chains. There is a 3-fold repeat in the folding of the polypeptide chain. Although this folding pattern suggests gene triplication, no significant internal sequence homology between topologically corresponding residues exists. The folding topology of interleukin-1β is very similar to that described by A. D. McLachlan [(1979) J. Mol. Biol. 133, 557–563] for soybean trypsin inhibitor.

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 Determination of the Three-dimensional Structure of Dislocations by Synchrotron White X-ray Topography Combined with a Topo-tomographic Technique

Materia Japan ◽  
2007 ◽  
Vol 46 (12) ◽  
pp. 823-823
Author(s):  
Seiji Kawado ◽  
Toshinori Taishi ◽  
Satoshi Iida ◽  
Yoshifumi Suzuki ◽  
Yoshinori Chikaura ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Tomographic Technique
Sign in / Sign up

Export Citation Format

Share Document