Biomedical subjects

Katarzyna Slepokura

Publications and source records attributed to Katarzyna Slepokura.

7 recordsLinked to original sources

PubMed2006

Different nucleobase orientations in two cyclic 2',3'-phosphates of purine ribonucleosides: Et(3)NH(2',3'-cAMP) and Et(3)NH(2',3'-cGMP)xH(2)O.

The crystal structures of triethylammonium adenosine cyclic 2',3'-phosphate {systematic name: triethylammonium 4-(6-aminopurin-9-yl)-6-hydroxymethyl-2-oxido-2-oxoperhydrofurano[3,4-c][1,3,2]dioxaphosphole}, Et(3)NH(2',3'-cAMP) or C(6)H(16)N(+).C(10)H(11)N(5)O(6)P(-), (I), and guanosine cyclic 2',3'-phosphate monohydrate {systematic name: triethylammonium 6-hydroxymethyl-2-oxido-2-oxo-4-(6-oxo-1,6-dihydropurin-9-yl)perhydrofurano[3,4-c][1,3,2]dioxaphosphole monohydrate}, [Et(3)NH(2',3'-cGMP)].H(2)O or C(6)H(16)N(+).C(10)H(11)N(5)O(7)P(-).H(2)O, (II), reveal different nucleobase orientations, viz. anti in (I) and syn in (II). These are stabilized by different inter- and intramolecular hydrogen bonds. The structures also exhibit different ribose ring puckering [(4)E in (I) and (3)T(2) in (II)] and slightly different 1,3,2-dioxaphospholane ring conformations, viz. envelope in (I) and puckered in (II). Infinite ribbons of 2',3'-cAMP(-) and helical chains of 2',3'-cGMP(-) ions, both formed by O-H...O, N-H...X and C-H...X (X = O or N) hydrogen-bond contacts, characterize (I) and (II), respectively.

Cyclic AMP↗

PubMed2006

[(5-Bromopyridinium-2-ylamino)(phosphono)methyl]phosphonate.

The title compound, C6H9BrN2O6P2, a micromolar inhibitor of the farnesyl pyrophosphate synthase, is a Z-isomer zwitterion with one negative phosphonate group and a protonated pyridine N atom. Two types of ribbons, both parallel to the a axis, formed by several centrosymmetrically related O-H...O and N-H...O hydrogen bonds are generated in the crystal structure. The resulting two-dimensional (001) "double-layered" networks are joined into a three-dimensional network via inversion-related halogen-oxygen interactions.

Crystallography↗

PubMed2006

Structure of dihydroxyacetone phosphate dimethyl acetal, a stable dihydroxyacetone phosphate precursor, in the crystalline state.

Crystal and molecular structures of four different salts of a dihydroxyacetone phosphate (DHAP) precursor, its dimethyl acetal [2,2-dimethoxy-1,3-propanediol phosphate, C(5)H(13)O(7)P, (MeO)(2)DHAP]: (cha)(2)[(MeO)(2)DHAP].H(2)O (6a), (cha)[(MeO)(2)DHAP] (6b), Na(2)[(MeO)(2)DHAP].5.75H(2)O (6c) and K(2)[(MeO)(2)DHAP].H(2)O (6d), along with the cyclohexylammonium (cha) salt of its phenyl ester (cha)[(MeO)(2)DHAP(Ph)] (6e) are described. In the (MeO)(2)DHAP mono- and dianions, slightly different orientation of the phosphate group in relation to the acetal carbon atom is observed, with a delicate tendency of phosphate group to be located antiperiplanar in the monoanions and anticlinal in the dianions. The 2,2-dimethoxy-1,3-propandiol moiety, (MeO)(2)DHA, seems to be very rigid and its conformation is independent of phosphorylation, the ionization state of the inserted phosphate group and its additional substitution. The overall structures of the cyclohexylammonium (6a,b) and potassium salts (6d) have a double-layered architecture, while the sodium cation network in 6c forms the system of channels, which are filled up with the [(MeO)(2)DHAP](2-) ions. The different architectures of 6c and 6d crystals result from the different ways in which the relevant dianions coordinate to sodium and potassium ions and affect also the hydrogen bonding system observed in 6c and 6d crystals.

Acetals↗

PubMed2005

The mimetics of antiadhesive peptides as the inhibitors of Mycobacterium kansasii phagocytosis.

The alpha-guanidino acids derived of 15 proteinaceous amino acids, omega-guanidino acids with gradually increased hydrocarbon chains, and amidinated dipeptides, were tested as the mimetics of antiadhesive peptides in Mycobacteria phagocytosis inhibition. The crystal structure of omega-guanidino acids used was determined by X-ray structural analysis. It follows from our experiments that the proper distance between guanidine and carboxyl groups of effector molecules is of decisive importance for their inhibitory activity.

Amidines↗

PubMed2004

Crystal structures of dihydroxyacetone and its derivatives.

The crystal and molecular structures of three crystalline forms of the dihydroxyacetone dimer, C6H12O6, DHA-dimer: alpha (1a), beta (1b), and gamma (1c), the hydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3)(2) x H2O, CaCl2(DHA)2 x H2O (2a), the tetrahydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3) x 4H2O, CaCl2(DHA) x 4H2O (2b), the dihydroxyacetone monomer, C3H6O3, DHA (2c), and dihydroxyacetone dimethyl acetal, C5H12O4, (MeO)2DHA (3) are described. Compounds 1a and 2b crystallize in the triclinic system, and 1b,c, 2a,c, and 3 are monoclinic. Molecules of all forms of dihydroxyacetone dimer 1a,b, and 1c are the trans isomers, with the 1,4-dioxane ring in the chair conformation and the hydroxyl and hydroxymethyl groups in axial and equatorial dispositions, respectively. The Ca2+ ions in 2a and 2b are bridged by the carbonyl O atoms from two symmetry-related DHA molecules to form centrosymmetric dimers with Ca...Ca distance of 4.307(2)A in 2a and 4.330(2) and 4.305(2)A in two crystallographically independent dimers in 2b. DHA molecules coordinate to the Ca2+ ions by hydroxyl and carbonyl oxygen atoms. The eight-coordinate polyhedra of Ca2+ are completed by water molecule and Cl- ion in 2a and by four water molecules in 2b. The dihydroxyacetone molecules in 2a,b, and 2c are in an extended conformation, with both hydroxyl groups being synperiplanar (sp) to the carbonyl O atom. All hydroxyl groups in 2c (along with water molecules in 2a and 2b) are involved as donors in medium strong and weak intermolecular O-H...O hydrogen bonding. Some of them, as well as carbonyl O atoms or Cl- ions in 2a and 2b, act as acceptors in C-H...O (and C-H...Cl) hydrogen interactions.

Crystallography, X-Ray↗

PubMed2004

5,5-Dimethoxy-2-phenoxy-1,3,2-dioxaphosphorinane 2-oxide.

In the title compound, C(11)H(15)O(6)P, the six-membered dioxaphosphorinane ring of the cyclic phosphate triester exists in a distorted chair conformation, with the phenoxy group in an axial position. The phenyl ring and both methoxy groups are in a trans-gauche orientation with respect to the 1,3,2-dioxaphosphorinane ring. In the phosphate group, a significant deformation from the ideal tetrahedral shape is observed. The crystal structure is stabilized by a three-dimensional network of C-H...O interactions.

Journal Article↗

PubMed2003

Polymeric bis(phosphonomethylcarboxylato)calcium(II) at 85 K.

In the crystal structure of the title compond, alternatively called poly[calcium(II)-di-mu-carboxymethylphosphonato], [Ca(C(2)H(4)O(5)P)(2)](n) or [Ca(H(2)AP)(2)](n), one of the phosphonate O atoms of the phosphonocarboxylate monoanion lies nearly antiperiplanar (ap) to the carboxylic acid C atom. The phosphonate P atom is located -sc and +ac relative to the carboxylic acid O atoms. The overall structure has a layered architecture. The Ca(2+) cations lie on a twofold axis and are bridged by the phosphonate O atoms to form chains along the c axis, giving layers parallel to (100). There are medium-strength O-H...O and C-H...O hydrogen-bonding interactions stabilizing the layers, and O-H...O hydrogen bonds connect adjacent layers.

Journal Article↗