The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (i) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (ii) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.

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Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B 6 and is an important cofactor for several of the enzymes involved in the metabolism of amine-containing natural products such as amino acids and amino-sugars. The PLP synthase holoenzyme consists of two subunits: YaaD catalyzes the condensation of ribulose 5-phosphate, glyceraldehyde-3-phosphate and ammonia and YaaE catalyzes the production of ammonia from glutamine. Here we describe the structure of the PLP synthase complex (YaaD-YaaE) from Thermotoga maritima at 2.9 Å resolution. This complex consists of a core of 12 YaaD monomers with 12 noninteracting YaaE monomers attached to the core. Compared to the previously published structure of PdxS (a YaaD ortholog in Geobacillus stearothermophilus), the N-terminus (1-18), which includes helix α0, the β2-α2 loop(46-56), which includes new helix α2a, and the C-terminus (270-280) of YaaD, are ordered in the complex but disordered in PdxS. A ribulose 5-phosphate is bound to YaaD via an imine with Lys82. Previous studies have demonstrated a similar imine at Lys149 and not at Lys81 (equivalent to Lys150 and 82 in T. maritima) for the Bacillus subtilis enzyme suggesting the possibility that two separate sites on YaaD are involved in PLP formation. A phosphate from the crystallization solution is found bound to YaaD and also serves as a marker for a possible second active site. An ammonia channel that connects the active site of YaaE with the ribulose 5-phosphate binding site was identified. This channel is similar to one found in imidazole glycerol phosphate synthase; however, when the β-barrels of the two complexes are superimposed, the glutaminase domains are rotated by about 180°w ith respect to each other.Pyridoxal 5'-phosphate (4, PLP) is the biologically active form of vitamin B 6 and is an important cofactor for several of the enzymes involved in the metabolism of amine-containing natural products such as amino acids and amino-sugars (1-4). There are two distinct PLP biosynthetic pathways that have not yet been found to coexist in the same organism (5). The Escherichia coli pathway has been extensively studied (6)(7)(8)(9)(10)(11)(12). In this pathway, PdxJ catalyzes the formation of pyridoxine 5'-phosphate (3, PNP) from 3-phosphohydroxy-1-aminoacetone 2 and 1-deoxy-D-xyulose 5-phosphate 1. This is then oxidized to PLP 4 by PdxH (Scheme 1).In the alternative pathway, PLP is formed from ribose 5-phosphate (5, R5P), glyceraldehyde 3-phosphate (6, G3P) and ammonia formed by the hydrolysis of glutamine (13-18) (Scheme 1 METHODS AND MATERIALS Molecular CloningStandard methods were used for DNA restriction endonuclease digestion, ligation and transformation of DNA. Genomic DNA and plasmid DNA were purified with a Wizard Plus SV genomic DNA kit and a DNA Miniprep kit (Promega), respectively. DNA fragments were separated by agarose gel electrophoresis, excised and purified with the QiaExII (Qiagen). E. coli strain DH5 α was used as a recipient for transformation during plasmid construction ...

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