Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystal structure of the ?-racemate of methohexital.

ABSTRACT: Mol-ecules of the title compound, C14H18N2O3 [systematic name: 5-allyl-5-(hex-3-yn-2-yl)-1-methylpyrimidine-2,4,6(1H,3H,5H)-trione in the (RbSh )/(SbRh ) racemic form], are connected by mutual N-H?O=C hydrogen bonds in which the carbonyl group at the 2-position of the pyrimidine-trione ring is employed. These inter-actions result in an inversion dimer which displays a central R 2 (2)(8) ring motif. This dimer is topologically distinct from that of the previously reported (SbRh ) form, which is, however, also based on an R 2 (2)(8) motif. The methyl group at the 1-position of the pyrimidine-trione ring in the title structure is disordered over two sets of sites in a 0.57?(2):0.43?(2) ratio.

SUBMITTER: Gelbrich T

PROVIDER: S-EPMC4384543 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystal structure of the α-racemate of methohexital.

Gelbrich Thomas T Griesser Ulrich J UJ

Acta crystallographica. Section E, Crystallographic communications 20150124 Pt 2

Mol-ecules of the title compound, C14H18N2O3 [systematic name: 5-allyl-5-(hex-3-yn-2-yl)-1-methylpyrimidine-2,4,6(1H,3H,5H)-trione in the (RbSh )/(SbRh ) racemic form], are connected by mutual N-H⋯O=C hydrogen bonds in which the carbonyl group at the 2-position of the pyrimidine-trione ring is employed. These inter-actions result in an inversion dimer which displays a central R 2 (2)(8) ring motif. This dimer is topologically distinct from that of the previously reported (SbRh ) form, which is, ...[more]

PMID: 25878820

Similar Datasets

Crystal orientation and crystal structure of paramagnetic α-Al under a pulsed electromagnetic field.

Project description:The intermittent electromagnetic fields with a large [Formula: see text] can enhance the properties of ferromagnetic materials and significantly affect paramagnetic materials. In this study, the effect of a pulsed electromagnetic field on the crystal orientation of the primary phase and microstructure evolution of an Al-Zn-Mg-Cu alloy was investigated. A mathematical model was developed to describe crystal rotation under a pulsed electromagnetic field. The model predictions show that the magnetic energy difference generated by the magnetic anisotropy of the primary crystal produces primary phases with sizes of 225-100 μm to rotate into a <111> preferred orientation. The lattice constant, the interplanar spacing, and the microstrain increase with the duty cycle of the pulsed magnetic field, especially for the (111) and (200) crystal planes. This study provides preliminary theoretical support for using pulsed electromagnetic fields to control the orientation and microscopic properties of materials.

| S-EPMC7326961 | biostudies-literature

Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.

Project description:The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and R(free) = 0.162. The average coordinate estimated standard deviations are 0.021 Angstrom and 0.038 Angstrom for backbone atoms and side-chain atoms, respectively. Besides providing a more precise view of the alpha-isoform than previously available, these data permit comparison with the 0.91 Angstrom structure determined for pike beta-parvalbumin. Visualization of the anisotropic displacement parameters as thermal ellipsoids yields insight into the atomic motion within the Ca(2+)-binding sites. The asymmetric unit includes three parvalbumin (PV) molecules. Interestingly, the EF site in one displays uncharacteristic flexibility. The ellipsoids for Asp-92 are particularly large and non-spherical, and the shape of the Ca(2+) ellipsoid implies significant vibrational motion perpendicular to the plane defined by the four y and z ligands. The relative dearth of crystal-packing interactions in this site suggests that the heightened flexibility may be the result of diminished intermolecular contacts. The implication is that, by impeding conformational mobility, crystal-packing forces may cause serious overestimation of EF-hand rigidity. The high quality of the data permitted 11 residues to be modeled in alternative side-chain conformations, including the two core residues, Ile-97 and Leu-105. The discrete disorder observed for Ile-97 may have functional ramifications, providing a mechanism for communicating binding status between the CD and EF binding loops and between the PV metal ion-binding domain and the N-terminal AB region.

| S-EPMC2279919 | biostudies-literature

Crystal structure of Saccharomyces cerevisiae Aro8, a putative α-aminoadipate aminotransferase.

Project description:α-Aminoadipate aminotransferase (AAA-AT) catalyzes the amination of 2-oxoadipate to α-aminoadipate in the fourth step of the α-aminoadipate pathway of lysine biosynthesis in fungi. The aromatic aminotransferase Aro8 has recently been identified as an AAA-AT in Saccharomyces cerevisiae. This enzyme displays broad substrate selectivity, utilizing several amino acids and 2-oxo acids as substrates. Here we report the 1.91Å resolution crystal structure of Aro8 and compare it to AAA-AT LysN from Thermus thermophilus and human kynurenine aminotransferase II. Inspection of the active site of Aro8 reveals asymmetric cofactor binding with lysine-pyridoxal-5-phosphate bound within the active site of one subunit in the Aro8 homodimer and pyridoxamine phosphate and a HEPES molecule bound to the other subunit. The HEPES buffer molecule binds within the substrate-binding site of Aro8, yielding insights into the mechanism by which it recognizes multiple substrates and how this recognition differs from other AAA-AT/kynurenine aminotransferases.

| S-EPMC3795499 | biostudies-literature

Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose.

Project description:The crystal structure of Bacillus subtilis alpha-amylase, in complex with the pseudotetrasaccharide inhibitor acarbose, revealed an hexasaccharide in the active site as a result of transglycosylation. After comparison with the known structure of the catalytic-site mutant complexed with the native substrate maltopentaose, it is suggested that the present structure represents a mimic intermediate in the initial stage of the catalytic process.

| S-EPMC262715 | biostudies-literature

Rerefinement of the crystal structure of α-ThBr<sub>4</sub>.

Project description:Single crystals of α-ThBr4, thorium(IV) tetra-bromide, were obtained as a side product from the reaction of CuBr with β-ThBr4 at 753 K. In the crystal structure, the Th atom (site symmetry ..) is surrounded by eight Br atoms in the form of a tetra-gonal-disphenoidal coordination polyhedron. The connectivity of these polyhedra is 3 ∞[ThBr4/2Br4/2]. In comparison with the previous crystal structure refinement [Mason et al. (1974 ▸). J. Less-Common Met. 35, 331-338], the current rerefinement resulted in much higher preciscion of the lattice parameters and the atomic coordinates.

| S-EPMC10626844 | biostudies-literature

The Crystal Structure of an Integral Membrane Fatty Acid α-Hydroxylase.

Project description:Neuronal electrical impulse propagation is facilitated by the myelin sheath, a compact membrane surrounding the axon. The myelin sheath is highly enriched in galactosylceramide (GalCer) and its sulfated derivative sulfatide. Over 50% of GalCer and sulfatide in myelin is hydroxylated by the integral membrane enzyme fatty acid 2-hydroxylase (FA2H). GalCer hydroxylation contributes to the compact nature of the myelin membrane, and mutations in FA2H result in debilitating leukodystrophies and spastic paraparesis. We report here the 2.6 Å crystal structure of sphingolipid α-hydroxylase (Scs7p), a yeast homolog of FA2H. The Scs7p core is composed of a helical catalytic cap domain that sits atop four transmembrane helices that anchor the enzyme in the endoplasmic reticulum. The structure contains two zinc atoms coordinated by the side chains of 10 highly conserved histidines within a dimetal center located near the plane of the cytosolic membrane. We used a yeast genetic approach to confirm the important role of the dimetal-binding histidines in catalysis and identified Tyr-322 and Asp-323 as critical determinants involved in the hydroxylase reaction. Examination of the Scs7p structure, coupled with molecular dynamics simulations, allowed for the generation of a model of ceramide binding to Scs7p. Comparison of the Scs7p structure and substrate-binding model to the structure of steroyl-CoA desaturase revealed significant differences in the architecture of the catalytic cap domain and location of the dimetal centers with respect to the membrane. These observations provide insight into the different mechanisms of substrate binding and recognition of substrates by the hydroxylase and desaturase enzymes.

| S-EPMC4705972 | biostudies-literature

Crystal structure of 6-de-oxy-α-l-psico-furan-ose.

Project description:The title compound, C6H12O5, was crystallized from an aqueous solution of 6-de-oxy-l-psicose (6-de-oxy-l-allulose, (3S,4S,5S)-1,3,4,5-tetra-hydroxy-hexan-2-one), and the mol-ecule was confirmed as α-furan-ose with a (3) T 4 (or E 4) conformation, which is a predominant tautomer in solution. This five-membered furan-ose ring structure is the second example in the field of the 6-de-oxy-ketohexose family. The cell volume of the title compound [742.67 (7) Å(3), Z = 4 at room temperature] is only 1.4% smaller than that of β-d-psico-pyran-ose, C6H12O6 (753.056 Å(3), Z = 4 at room temperature).

| S-EPMC4719940 | biostudies-literature

Crystal structure of methyl α-l-rhamno-pyranosyl-(1→2)-α-l-rhamno-pyran-oside monohydrate.

Project description:The title compound, C13H24O9·H2O, a structural model for part of bacterial O-anti-gen polysaccharides from Shigella flexneri and Escherichia coli, crystallizes with four independent disaccharide mol-ecules and four water mol-ecules in the asymmetric unit. The conformation at the glycosidic linkage joining the two rhamnosyl residues is described by the torsion angles φH of 39, 30, 37 and 37°, and ψH of -32, -35, -31 and -32°, which are the major conformation region known to be populated in an aqueous solution. The hexo-pyran-ose rings have the 1 C 4 chair conformation. In the crystal, the disaccharide and water mol-ecules are associated through O-H⋯O hydrogen bonds, forming a layer parallel to the bc plane. The layers stack along the a axis via hydro-phobic inter-actions between the methyl groups.

| S-EPMC6658941 | biostudies-literature

Redetermined crystal structure of α-dl-me-thio-nine at 340 K.

Project description:Two forms, α and β, are known for the racemic amino acid dl-me-thio-nine, C5H11NO2S. The phase transition between them, taking place around 326 K, is associated with sliding at the central inter-faces of the hydro-phobic regions in the crystal, leaving the hydrogen-bonding pattern unperturbed. For the high-temperature α phase, only a structure of rather low quality has been available [R factor = 0.118, no H-atom coordinates; Taniguchi et al. (1980 ▶). Bull. Chem. Soc. Jpn, 53, 803-804]. We here present accurate structural data for this polymorph [R(F) = 0.049], which are compared with other related amino acid structures with similar properties. We report for the first time that the side chain of this phase has a minor disorder component [occupancy 0.0491 (18)] with a gauche+ rather than a gauche- conformation for the N-C-C-C group. In the crystal of the title compound, N-H⋯O hydrogen bonds link the mol-ecules into (100) sheets.

| S-EPMC4257343 | biostudies-literature

Redetermined crystal structure of N-(β-carb-oxy-eth-yl)-α-isoleucine.

Project description:Redetermination of the crystal structure of N-(β-carb-oxy-eth-yl)-α-isoleucine, C9H18N2O3, reported earlier by Nehls et al. [Acta Cryst. (2013), E69, o172-o173], was undertaken in which the ionization state assigned to the mol-ecule as unionized has been modified as zwitterionic in the present work. Single-crystal X-ray intensity data obtained from freshly grown crystals and freely refining the amino H atoms provide enhanced refinement and structural parameters, particularly the hydrogen-bonding scheme. N-H⋯O hydrogen bonds dominate the inter-molecular inter-actions along with a C-H⋯O hydrogen bond. The inter-molecular inter-action pattern is a three-dimensional network. The structure was refined as a two-component perfect inversion twin.

| S-EPMC4555364 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data