Crystal structures of two formamidinium hexa-fluorido-phosphate salts, one with batch-dependent disorder.

Cytochrome P450 46A1 (CYP46A1) initiates the major pathway of cholesterol elimination from the brain and thereby controls cholesterol turnover in this organ. We determined x-ray crystal structures of CYP46A1 in complex with four structurally distinct pharmaceuticals; antidepressant tranylcypromine (2.15 Å), anticonvulsant thioperamide (1.65 Å), antifungal voriconazole (2.35 Å), and antifungal clotrimazole (2.50 Å). All four drugs are nitrogen-containing compounds that have nanomolar affinity for CYP46A1 in vitro yet differ in size, shape, hydrophobicity, and type of the nitrogen ligand. Structures of the co-complexes demonstrate that each drug binds in a single orientation to the active site with tranylcypromine, thioperamide, and voriconazole coordinating the heme iron via their nitrogen atoms and clotrimazole being at a 4 Å distance from the heme iron. We show here that clotrimazole is also a substrate for CYP46A1. High affinity for CYP46A1 is determined by a set of specific interactions, some of which were further investigated by solution studies using structural analogs of the drugs and the T306A CYP46A1 mutant. Collectively, our results reveal how diverse inhibitors can be accommodated in the CYP46A1 active site and provide an explanation for the observed differences in the drug-induced spectral response. Co-complexes with tranylcypromine, thioperamide, and voriconazole represent the first structural characterization of the drug binding to a P450 enzyme.

Prokaryotic glutathione S-transferases are as diverse as their eukaryotic counterparts but are much less well characterized. BphK from Burkholderia xenovorans LB400 consumes two GSH molecules to reductively dehalogenate chlorinated 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), inhibitory polychlorinated biphenyl metabolites. Crystallographic structures of two ternary complexes of BphK were solved to a resolution of 2.1A. In the BphK-GSH-HOPDA complex, GSH and HOPDA molecules occupy the G- and H-subsites, respectively. The thiol nucleophile of the GSH molecule is positioned for SN2 attack at carbon 3 of the bound HOPDA. The respective sulfur atoms of conserved Cys-10 and the bound GSH are within 3.0A, consistent with product release and the formation of a mixed disulfide intermediate. In the BphK-(GSH)2 complex, a GSH molecule occupies each of the two subsites. The three sulfur atoms of the two GSH molecules and Cys-10 are aligned suitably for a disulfide exchange reaction that would regenerate the resting enzyme and yield disulfide-linked GSH molecules. A second conserved residue, His-106, is adjacent to the thiols of Cys-10 and the GSH bound to the G-subsite and thus may stabilize a transition state in the disulfide exchange reaction. Overall, the structures support and elaborate a proposed dehalogenation mechanism for BphK and provide insight into the plasticity of the H-subsite.

The title compound, C20H14I2N2O2, a di-iodo-Schiff base, crystallizes in space group Pbca with one mol-ecule per asymmetric unit. The mol-ecular structure reveals two intra-molecular O-H⋯N hydrogen bonds that give the mol-ecule a twisted structure with non-coplanar rings. In the crystal structure, the mol-ecular packing is stabilized by π-π stacking, hydrogen- and halogen-bonding (C-H⋯I; O⋯I) inter-actions.

The cyclohexane-1,2,3,4,5-pentol,C6H12O5 is a natural product extracted from Adiscanthus fusciflorus (Rutaceae). It crystallizes in the non-centrosymmetric space group P21 with one molecule in the asymmetric unit and it has been postulated to have at least ten strong O-H…O intermolecular interactions, two per each OH group of one molecule, producing a three-dimensional network. The crystal packing is defined by O-H…O hydrogen bonds. Due to the crucial role of the hydrogen bonds in defining the crystal structure, theoretical investigations in the gas phase have been carried out in order to explore the hydrogenbonding mechanism through a quantitative Kohn-Sham molecular orbital and corresponding energy decomposition analyses. The existence of a covalent component in hydrogen bonds has been proved which originates from donor-acceptor orbital interactions in the σ-electron system. Our analyses show that the stability of the crystal structure is enhanced by the formation of two hydrogen bonds with two vicinal molecules for each OH group in C6H12O5 molecule with respect to the formation of one or two hydrogen bonds with only one vicinal molecule, thus confirming the proposed existence of ten strong O-H…O intermolecular interactions for each molecule in the asymmetric unit. The presence of a cooperativity effect is observed which originates from a charge separation induced by the two vicinal molecules hydrogenbonded to an OH group in C6H12O5 molecule.

The title compound, C17H16O3S, crystallized with two independent mol­ecules (A and B) in the asymmetric unit. The dihedral angle between the benzo­furan ring system [r.m.s. deviation of 0.013 (1) for A and 0.009 (1) Å for B] and the 2-methyl­phenyl ring is 83.88 (5) for A and 86.94 (5)° for B. In the crystal, the B mol­ecules are linked into a chain along the b-axis direction by C—H⋯O hydrogen bonds. The A mol­ecules are connected on either side of this chain by further C—H⋯O hydrogen bonds. These chains are linked via C—H⋯π inter­actions, forming sheets parallel to (100). There are also very weak π–π inter­actions present [centroid–centroid distance = 3.925 (11) Å] involvingthe 2-methyl­phenyl rings of neighbouring A and B mol­ecules.

The title compound, C(9)H(7)NO, has two symmetry-independent molecules in the asymmetric unit, which have different conformations of the hydroxy group with respect to the quinoline ring. One of the molecules adopts a cis conformation, while the other shows a trans conformation. Each type of independent molecule links into a separate infinite O-H...N hydrogen-bonded chain with the graph-set notation C(7). These chains are perpendicular in the unit cell, one extended in the a-axis direction and the other in the b-axis direction. There is also a weak C-H...O hydrogen bond with graph-set notation D(2), which runs in the c-axis direction and joins the two separate O-H...N chains. The significance of this study lies in the comparison drawn between the experimental and calculated data of the crystal structure of the title compound and the data of several other derivatives possessing the hydroxy group or the quinoline ring. The correlation between the IR spectrum of this compound and the hydrogen-bond energy is also discussed.

Recognition of poly(C) DNA and RNA sequences in mammalian cells is achieved by a subfamily of the KH (hnRNP K homology) domain-containing proteins known as poly(C)-binding proteins (PCBPs). To reveal the molecular basis of poly(C) sequence recognition, we have determined the crystal structure, at 1.7-A resolution, of PCBP2 KH1 in complex with a 7-nucleotide DNA sequence (5'-AACCCTA-3') corresponding to one repeat of the human C-rich strand telomeric DNA. The protein-DNA interaction is mediated by the combination of several stabilizing forces including hydrogen bonding, electrostatic interactions, van der Waals contacts, and shape complementarities. Specific recognition of the three cytosine residues is realized by a dense network of hydrogen bonds involving the side chains of two conserved lysines and one glutamic acid. The co-crystal structure also reveals a protein-protein dimerization interface of PCBP2 KH1 located on the opposite side of the protein from the DNA binding groove. Numerous stabilizing protein-protein interactions, including hydrophobic contacts, stacking of aromatic side chains, and a large number of hydrogen bonds, indicate that the protein-protein interaction interface is most likely genuine. Interaction of PCBP2 KH1 with the C-rich strand of human telomeric DNA suggests that PCBPs may participate in mechanisms involved in the regulation of telomere/telomerase functions.

The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.

Oxalate oxidase (EC 1.2.3.4) catalyzes the conversion of oxalate and dioxygen to hydrogen peroxide and carbon dioxide. In this study, glycolate was used as a structural analogue of oxalate to investigate substrate binding in the crystalline enzyme. The observed monodentate binding of glycolate to the active site manganese ion of oxalate oxidase is consistent with a mechanism involving C-C bond cleavage driven by superoxide anion attack on a monodentate coordinated substrate. In this mechanism, the metal serves two functions: to organize the substrates (oxalate and dioxygen) and to transiently reduce dioxygen. The observed structure further implies important roles for specific active site residues (two asparagines and one glutamine) in correctly orientating the substrates and reaction intermediates for catalysis. Combined spectroscopic, biochemical, and structural analyses of mutants confirms the importance of the asparagine residues in organizing a functional active site complex.

The L1 family neural cell adhesion molecules play key roles in specifying the formation and remodeling of the neural network, but their homophilic interaction that mediates adhesion is not well understood. We report two crystal structures of a dimeric form of the headpiece of neurofascin, an L1 family member. The four N-terminal Ig-like domains of neurofascin form a horseshoe shape, akin to several other immunoglobulin superfamily cell adhesion molecules such as hemolin, axonin, and Dscam. The neurofascin dimer, captured in two crystal forms with independent packing patterns, reveals a pair of horseshoes in trans-synaptic adhesion mode. The adhesion interaction is mediated mostly by the second Ig-like domain, which features an intermolecular β-sheet formed by the joining of two individual GFC β-sheets and a large but loosely packed hydrophobic cluster. Mutagenesis combined with gel filtration assays suggested that the side chain hydrogen bonds at the intermolecular β-sheet are essential for the homophilic interaction and that the residues at the hydrophobic cluster play supplementary roles. Our structures reveal a conserved homophilic adhesion mode for the L1 family and also shed light on how the pathological mutations of L1 affect its structure and function.

Dichlorodiazadienes were synthesized based on 4-methylbenzaldehyde, the structures of some compounds were confirmed via the X-ray method and a series of crystallographic properties, the role of non-covalent interactions in the forming of crystal, and (using Hirshfeld surface analysis) intermolecular interactions were studied. It was determined that as the result of the impact of nitro-group on the direction of the reactions of (E)-1-(4-methylbenzylydene)-2-(4-nitrophenyl)-hidrazone with CCl4 and CBr4, reaction by-products E)-1-(4-nitrophenyl)-2-(1,1,1-trichloro-2-methylpropan-2-yl)diazene, (Z)-4-methyl-N-(4nitrophenyl)benzohydra-zonoyl chloride and (Z)-4-methyl-N-(4-nitrophenyl)benzohydrazonoylbromide had been formed. While (E)-1-(2,2-dichloro-1-(p-tolyl)vinyl)-2-(3,4-dimethylphenyl)diazene crystallizes in the monoclinic P21/n space group with Z = 4, (E)-4-((2,2-dichloro-1-(p-tolyl)vinyl)diazenyl) benzonitrile crystallizes in the monoclinic Cc space group with four independent molecules (I, II, III and IV) in the asymmetric unit (Z = 16), and (E)-1-(4-nitrophenyl)-2-(1,1,1-trichloro-2-methylpropan-2-yl)diazene and (Z)-4-methyl-N-(4-nitrophenyl)benzohydrazonoylbromide crystallize in the monoclinic P21/c space group with Z = 4. The molecules in the crystal of (E)-1-(2,2-dichloro-1-(p-tolyl)vinyl)-2-(3,4-dimethylphenyl)diazene are linked into infinite three-dimensional network by C−H···N of hydrogen bonds, C---H…p and C---Cl…p interaction. In the crystal of the (E)-4-((2,2-dichloro-1-(p-tolyl)vinyl)diazenyl) benzonitrile, while molecules are linked in layers parallel to the (200) plane by intermolecular C---H...N hydrogen bonds and C---H...p interactions, in the crystal of the (E)-1-(4-nitrophenyl)-2-(1,1,1-trichloro-2-methylpropan-2-yl)diazene, the molecules are connected in layers parallel to the (10-2) plane by intermolecular C---H...O hydrogen bonds, C---Cl... p and p-p interactions, and in the crystal of the (Z)-4-methyl-N-(4-nitrophenyl)benzohydrazonoylbromide, the molecules are connected in layers parallel to the (020) plane by intermolecular C---H...O and N---H...O hydrogen bonds and C--O...p interactions. These layers bond with van der Waals interactions, strengthening the crystal structure.

The important role of the serine/threonine protein phosphatase 2A (PP2A) in various cellular processes requires a precise and dynamic regulation of PP2A activity, localization, and substrate specificity. The regulation of the function of PP2A involves the reversible methylation of the COOH group of the C-terminal leucine of the catalytic subunit, which, in turn, controls the enzyme's heteromultimeric composition and confers different protein recognition and substrate specificity. We have determined the structure of PPM1, the yeast methyltransferase responsible for methylation of PP2A. The structure of PPM1 reveals a common S-adenosyl-l-methionine-dependent methyltransferase fold, with several insertions conferring the specific function and substrate recognition. The complexes with the S-adenosyl-l-methionine methyl donor and the S-adenosyl-l-homocysteine product and inhibitor unambiguously revealed the co-substrate binding site and provided a convincing hypothesis for the PP2A C-terminal peptide binding site. The structure of PPM1 in a second crystal form provides clues to the dynamic nature of the PPM1/PP2A interaction.

1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C16H16N2O3S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C11H14N2O2S, (II), have been synthesized and characterized. Compound (I) crystallizes in the space group P-1, while (II) crystallizes in the space group P21/c. In both structures, intramolecular N-H...O hydrogen bonding is present. The resulting six-membered pseudo-rings are quasi-aromatic and, in each case, interact with phenyl rings via stacking-type interactions. C-H...O, C-H...S and C-H...π interactions are also present. In (I), there is one molecule in the asymmetric unit. Pairs of molecules are connected via two intermolecular N-H...S hydrogen bonds, forming centrosymmetric dimers. In (II), there are two symmetry-independent molecules that differ mainly in the relative orientations of the phenyl rings with respect to the thiourea cores. Additional strong hydrogen-bond donor and acceptor -OH groups participate in the formation of intermolecular N-H...O and O-H...S hydrogen bonds that join molecules into chains extending in the [001] direction.

In the crystal structure of the title compound, C11H15N3O2S, mol­ecules are linked by pairs of N—H⋯O and O—H⋯S hydrogen, forming inversion dimers. These dimers are linked by N—H⋯S hydrogen bonds, forming double-stranded chains propagating along the b-axis direction. The two C atoms of the end chain of the mol­ecule are disordered over two sets os sites [occupancy ratio 0.574 (9):0.426 (9)].

The structures of three compounds of 3-chloro-2-nitro-benzoic acid with 5-nitro-quinoline, (I), 6-nitro-quinoline, (II), and 8-hy-droxy-quinoline, (III), have been determined at 190 K. In each of the two isomeric compounds, (I) and (II), C7H4ClNO4·C9H6N2O2, the acid and base mol-ecules are held together by O-H⋯N and C-H⋯O hydrogen bonds. In compound (III), C9H8NO+·C7H3ClNO4 -, an acid-base inter-action involving H-atom transfer occurs and the H atom is located at the N site of the base mol-ecule. In the crystal of (I), the hydrogen-bonded acid-base units are linked by C-H⋯O hydrogen bonds, forming a tape structure along the b-axis direction. Adjacent tapes, which are related by a twofold rotation axis, are linked by a third C-H⋯O hydrogen bond, forming wide ribbons parallel to the (03) plane. These ribbons are stacked via π-π inter-actions between the quinoline ring systems [centroid-centroid distances = 3.4935 (5)-3.7721 (6) Å], forming layers parallel to the ab plane. In the crystal of (II), the hydrogen-bonded acid-base units are also linked into a tape structure along the b-axis direction via C-H⋯O hydrogen bonds. Inversion-related tapes are linked by further C-H⋯O hydrogen bonds to form wide ribbons parallel to the (08) plane. The ribbons are linked by weak π-π inter-actions [centroid-centroid distances = 3.8016 (8)-3.9247 (9) Å], forming a three-dimensional structure. In the crystal of (III), the cations and the anions are alternately linked via N-H⋯O and O-H⋯O hydrogen bonds, forming a 21 helix running along the b-axis direction. The cations and the anions are further stacked alternately in columns along the a-axis direction via π-π inter-actions [centroid-centroid distances = 3.8016 (8)-3.9247 (9) Å], and the mol-ecular chains are linked into layers parallel to the ab plane through these inter-actions.