trans-Di-aqua-tetra-kis-(tetra-hydro-furan-κO)iron(II) µ-carbonyl-tetra-deca-carbonyl-tetra-chlorido-µ-di-methyl-silanediolato-tetra-galliumtetra-iron(7 Ga-Fe)(Fe-Fe) tetra-hydro-furan tetrasolvate.

The title compound, [Fe(C4H8O)4(H2O)2][Fe4Ga4(C2H6O2Si)Cl4(CO)15]·4C4H8O, consists of an iron(II) cation octa-hedrally coordinated by two water mol-ecules (trans) with four tetra-hydro-furans (THF) at equatorial sites. Two additional THF mol-ecules are hydrogen bonded to each of the water mol-ecules. The dianion of the title compound is an organometallic butterfly complex with a dimethyl siloxane core and two iron-gallium fragments. The lengths of the iron to gallium metal-metal bonds range from 2.3875 (6) to 2.4912 (6) Å.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.

Sandwich compounds of cyanotrispyrazolylborates: complexation-induced ligand isomerization.

Reaction of the new cyanoscorpionate ligand, hydrotris(4-cyano-3-phenyl)pyrazolylborate (Tp(Ph),(4CN)) with Co(II), Mn(II), and Fe(II) unexpectedly results in the isolation only of crystals containing sandwich complexes in which the ligands have been isomerized to produce the heterocyanoscorpionate hydrobis(4-cyano-3-phenylpyrazolyl)(4-cyano-5-phenylpyrazolyl)borate (Tp(Ph),(4CN*)). The three complexes have been characterized crystallographically and are isostructural, with each ligand acting in a tridentate manner toward the metal. The isomerization of the ligand appears to be more facile than that of the analogous non-cyano ligand, Tp(Ph), with which crystals of the unisomerized sandwich compound have been isolated for Mn(II) and Fe(II).

Nickel(II), copper(II) and zinc(II) binding properties and cytotoxicity of tripodal, hexadentate tris(ethylenediamine)--analogue chelators.

Three tripodal hexamine chelators based on cis,cis-1,3,5-triaminocyclohexane (tach) have been synthesized and their aqueous coordination chemistry with Ni(II), Cu(II) and Zn(II) is reported. The chelators have a 2-aminoethyl pendant arm attached to each nitrogen of tach, specifically 'tachen'(N,N',N''-tris(2-aminoethyl)cyclohexane-cis,cis-1,3,5-triamine), and two with S,S,S-chiral pendant arms, 'tachpn'(N,N',N''-tris(2-aminopropyl)cyclohexane-cis,cis-1,3,5-triamine) and 'tachbn'(N,N',N''-tris(2-amino-3-phenylpropyl)cyclohexane-cis,cis-1,3,5-triamine. These chelators complex Ni(II), Cu(II) and Zn(II) in aqueous or aqueous/methanolic medium. The crystalline products [M(II)L](X)2 are isolated, where M = Ni(II), Cu(II) or Zn(II), L = tachen, tachpn or tachbn, and X = ClO4-. Crystallographic study of selected tachpn and tachbn complexes shows the chelate arms are constrained in a Lambda(deltadeltadelta) configuration about M(II), which is attributed to their chirality. Solution UV-vis spectroscopy of the Ni(II) and Cu(II) complexes indicates six-coordination and little effect of the pendant arm substitution on ligand-field strength. The single exception is [Cu(tachbn)]2+, whose spectrum is consistent with five-coordination in solution. The cytotoxicities of tachen, tachpn and tachbn toward cultured cancer cells is in the order tachen < tachpn < tachbn < tachpyr, where tachpyr is the aminopyridyl chelator N,N',N''-tris(2-pyridylmethyl)cyclohexane-cis,cis-1,3,5-triamine. The cytotoxicity difference is attributed to an order of increasing lipophilicity, tachen < tachpn < tachbn.

Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide.

We have determined the crystal structures of the ligand binding domain (LBD) of the rat vitamin D receptor in ternary complexes with a synthetic LXXLL-containing peptide and the following four ligands: 1alpha,25-dihydroxyvitamin D(3); 2-methylene-19-nor-(20S)-1alpha,25-dihydroxyvitamin D(3) (2MD); 1alpha-hydroxy-2-methylene-19-nor-(20S)-bishomopregnacalciferol (2MbisP), and 2alpha-methyl-19-nor-1alpha,25-dihydroxyvitamin D(3) (2AM20R). The conformation of the LBD is identical in each complex. Binding of the 2-carbon-modified analogues does not change the positions of the amino acids in the ligand binding site and has no effect on the interactions in the coactivator binding pocket. The CD ring of the superpotent analogue, 2MD, is tilted within the binding site relative to the other ligands in this study and to (20S)-1alpha,25-dihydroxyvitamin D(3) [Tocchini-Valentini et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 5491-5496]. The aliphatic side chain of 2MD follows a different path within the binding site; nevertheless, the 25-hydroxyl group at the end of the chain occupies the same position as that of the natural ligand, and the hydrogen bonds with histidines 301 and 393 are maintained. 2MbisP binds to the receptor despite the absence of the 25-hydroxyl group. A water molecule is observed between His 301 and His 393 in this structure, and it preserves the orientation of the histidines in the binding site. Although the alpha-chair conformer is highly favored in solution for the A ring of 2AM20R, the crystal structures demonstrate that this ring assumes the beta-chair conformation in all cases, and the 1alpha-hydroxyl group is equatorial. The peptide folds as a helix and is anchored through hydrogen bonds to a surface groove formed by helices 3, 4, and 12. Electrostatic and hydrophobic interactions between the peptide and the LBD stabilize the active receptor conformation. This stablization appears necessary for crystal growth.

Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica.

The three-dimensional structure of the pyridoxal 5'-phosphate (PLP)-dependent L-threonine-O-3-phosphate decarboxylase (CobD) from Salmonella enterica is described here. This enzyme is responsible for synthesizing (R)-1-amino-2-propanol phosphate which is the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. The molecule is a molecular dimer where each subunit consists of a large and small domain. Overall the protein is very similar to the members of the family of aspartate aminotransferases. Indeed, the arrangement of the ligands surrounding the cofactor and putative substrate binding site are remarkably close to that observed in histidinol phosphate aminotransferase, which suggests that this latter enzyme might have been its progenitor. The only significant differences in structure occur at the N-terminus, which is approximately 12 residues shorter in CobD and does not form the same type of interdomain interaction common to other aminotransferases. CobD is unusual since within the aspartate aminotransferase subfamily of PLP-dependent enzymes the chemical transformations are substantially conserved, where the only exceptions are 1-aminocyclopropane-1-carboxylate synthase and CobD. Although there are a large number of PLP-dependent amino acid decarboxylases, these are generally larger and structurally distinct from the members of the aspartate aminotransferase subfamily of enzymes. The structure of CobD suggests that the chemical fate of the external aldimine can be redirected by modifications at the N-terminus of the protein. This study provides insight into the evolutionary history of the cobalamin biosynthetic pathway and raises the question of why most PLP-dependent decarboxylases are considerably larger enzymes.

Transition Metal Complexes of p-Sulfonatocalix[5]arene.

The X-ray crystal structure of the p-sulfonatocalix[5]arene(5)(-) anion (1b) in the form of the dimeric hydrate Na(10)[p-sulfonatocalix[5]arene](2).33.5H(2)O (2) is reported. The reactions of 1b with a number of transition metal salts to form transition metal bridged bis(calixarene) inclusion complexes have also been investigated. The X-ray crystal structure of the "Co(H(2)O)(4)(2+)" bridged species Na(8)[Co(H(2)O)(4)(p-sulfonatocalix[5]arene)(2)].2CH(3)C(O)N(CH(3))(2).37H(2)O (3) which incorporates a "supercavity" large enough to encompass 2 N,N-dimethylacetamide (dma) guest molecules as well as ca. 15 water molecules and Na(+) ions is reported. Crystal data are as follows: for 2, monoclinic space group P2(1)/c, Z = 4, a = 22.0644(4), b = 19.1180(3), c = 27.7834(4) Å, beta = 91.780(1), V = 11714.1(5) Å(3); complex 3, orthorhombic space group Pnma, Z = 4, a = 22.2271(5), b = 30.1693(6), c = 18.8503(4) Å, V = 12640.6(5) Å(3).