1-(2-Naphth­yl)-3-phenyl-3-(4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one

In the title compound, C25H22N2OSe, the fused six-membered cyclo­hexene ring of the 4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazole group adopts a near half-chair conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.004 Å). There are weak inter­molecular C—H⋯O and C—H⋯π inter­actions in the crystal structure. Inter­molecular π–π stacking is also observed between the naphthyl units, with a centroid–centroid distance of 3.529 (15) Å

Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association

The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its homologue from Mycobacterium tuberculosis, indicating that the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer are characteristic features of mycobacterial SSBs. The central OB fold is conserved in mycobacterial SSBs as well as those from Escherichia coli, Deinococcus radiodurans and human mitochondria. However, the quaternary structure exhibits considerable variability. The observed plasticity of the subunit is related to this variability. The crystal structures and modelling provide a rationale for the variability. The strand involved in the clamp mechanism, which leads to higher stability of the tetramer, appears to occur in all high-G+C Gram-positive bacteria. The higher stability is perhaps required by these organisms. The mode of DNA binding of mycobacterial SSBs is different from that of E. coli SSB partly on account of the difference in the shape of the tetramers. Another difference between the two modes is that the former contains additional ionic interactions and is more susceptible to salt concentration

Structural Determination of Functional Units of the Nucleotide Binding Domain (NBD94) of the Reticulocyte Binding Protein Py235 of Plasmodium yoelii

Invasion of the red blood cells (RBC) by the merozoite of malaria parasites involves a large number of receptor ligand interactions. The reticulocyte binding protein homologue family (RH) plays an important role in erythrocyte recognition as well as virulence. Recently, it has been shown that members of RH in addition to receptor binding may also have a role as ATP/ADP sensor. A 94 kDa region named Nucleotide-Binding Domain 94 (NBD94) of Plasmodium yoelii YM, representative of the putative nucleotide binding region of RH, has been demonstrated to bind ATP and ADP selectively. Binding of ATP or ADP induced nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94, and directly impacted on the RBC binding ability of RH.In order to find the smallest structural unit, able to bind nucleotides, and its coupling module, the hinge region, three truncated domains of NBD94 have been generated, termed NBD94(444-547), NBD94(566-663) and NBD94(674-793), respectively. Using fluorescence correlation spectroscopy NBD94(444-547) has been identified to form the smallest nucleotide binding segment, sensitive for ATP and ADP, which became inhibited by 4-Chloro-7-nitrobenzofurazan. The shape of NBD94(444-547) in solution was calculated from small-angle X-ray scattering data, revealing an elongated molecule, comprised of two globular domains, connected by a spiral segment of about 73.1 A in length. The high quality of the constructs, forming the hinge-region, NBD94(566-663) and NBD94(674-793) enabled to determine the first crystallographic and solution structure, respectively. The crystal structure of NBD94(566-663) consists of two helices with 97.8 A and 48.6 A in length, linked by a loop. By comparison, the low resolution structure of NBD94(674-793) in solution represents a chair-like shape with three architectural segments.These structures give the first insight into how nucleotide binding impacts on the overall structure of RH and demonstrates the potential use of this region as a novel drug target

Epitope-Based Immunoinformatics and Molecular Docking Studies of Nucleocapsid Protein and Ovarian Tumor Domain of Crimean–Congo Hemorrhagic Fever Virus

Crimean–Congo hemorrhagic fever virus (CCHFV), the fatal human pathogen is transmitted to humans by tick bite, or exposure to infected blood or tissues of infected livestock. The CCHFV genome consists of three RNA segments namely, S, M, and L. The unusual large viral L protein has an ovarian tumor (OTU) protease domain located in the N terminus. It is likely that the protein may be autoproteolytically cleaved to generate the active virus L polymerase with additional functions. Identification of the epitope regions of the virus is important for the diagnosis, phylogeny studies, and drug discovery. Early diagnosis and treatment of CCHF infection is critical to the survival of patients and the control of the disease. In this study, we undertook different in silico approaches using molecular docking and immunoinformatics tools to predict epitopes which can be helpful for vaccine designing. Small molecule ligands against OTU domain and protein–protein interaction between a viral and a host protein have been studied using docking tools

4-{(4-Chloro­phen­yl)[4-(4-methyl­phen­yl)-1,2,3-selenadiazol-5-yl]meth­yl}-4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazole

In the title compound, C22H19ClN4Se2, the mean plane of the non-fused selenadiazole ring forms dihedral angles of 54.20 (16)° and 70.48 (11)°, respectively, with the essentially planar [maximum deviations of 0.025 (5) and 0.009 (2) Å, respectively] methyl­phenyl and chloro­phenyl substituents. The tetra­hydro-1,2,3-benzoselenadiazole group is disordered over two sets of sites with a refined occupancy ratio of 0.802 (5):0.198 (5). In the crystal, weak inter­molecular C—H⋯N inter­actions are observed

3-(4-Methyl­phen­yl)-1-phenyl-3-(4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one

In the title compound, C22H22N2OSe, the fused six-membered ring of the 4,5,6,7-tetra­hydro­benzo[d][1,2,3] selenadiazole group adopts a near to envelope (E form) conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.0059 Å). In the crystal, adjacent mol­ecules are inter­linked through weak inter­molecular C—H⋯π inter­actions

Crystal and Molecular Structure of an Acridinedione

The title compound, 10-(4-hydroxybenzoylamino)-3,4,6,7,9,10-hexahydro-1,8-(2H,5H)-acridinedione monohydrate, C_20H_2_2N_2O_4.H_2O, consists of partially hydrogenated acridine moiety with one benzoylamino substituent on the central ring. The compound crystallizes in monoclinic system with P21/c space group and the unit cell constants are: a = 11.142(4), b = 12.266(2), c = 13.320(2) $A^o$; \beta = 91.76(2)° and V = 1819.6(8) $A^3$. The central ring (B) adopts boat and the outer rings (A and C) adopt sofa conformations. The water molecule takes part in OW-H...O and N-H...OW hydrogen bond formation with acridinedione and benzoylamino group. The oxygen atom O1 interacts through O-H...O bond with the hydroxyl group and in a head-to-tail link up of molecules that results in the formation of an infinite supra molecular chain

NIMS: a database on nucleobase compounds and their interactions in macromolecular structures

The intense exploration of nucleotide-binding protein structures has created a whirlwind in the field of structural biology and bioinformatics. This has led to the conception and birth of NIMS. This database is a collection of detailed data on the nucleobases, nucleosides and nucleotides, along with their analogues as well as the protein structures to which they bind. Interaction details such as the interacting residues and all associated values have been made available. As a pioneering step, the diffraction precision index for protein structures, the atomic uncertainty for each atom, and the computed errors on the interatomic distances and angles are available in the database. Apart from the above, provision has been made to visualize the three-dimensional structures of both ligands and protein-ligand structures and their interactions in Jmol as well as JSmol. One of the salient features of NIMS is that it has been interfaced with a user-friendly and query-based efficient search engine. It was conceived and developed with the aim of serving a significant section of researchers working in the area of protein and nucleobase complexes. NIMS is freely available online at http://iris.physics.iisc.ernet.in/nims and it is hoped that it will prove to be an invaluable asset