Target-+Cyclooxygenase-2+(Francisella+tularensis)


 * //Francisella tularensis //****Cyclooxygenase-2 **


 * PDB/DOI: **[|10.2210/pdb5cox/pdb]


 * *RefSeq#: ** **NP_000954 **

 ***Organism (including strain):** **//Francisella tularensis //**


 * Etiologic Risk Group: ****Class A “Select Agent” **

 ***Disease Information (sort of like the Intro to your Mini-up):** **//Francisella tularensis //**** is a pathogenic species of Gram-negative bacteria and the causative agent of ** [|**tularemia**]**, the pneumonic form of which is often lethal without treatment. It is a fastidious, facultative ** [|**intracellular**] **bacterium which requires ** [|**cysteine**] **for growth. **[|**[1**]] **<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Due to its low infectious dose, ease of spread by aerosol and high ** [|**virulence**]**<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">, //F. tularensis// is classified as a Class A Select Agent by the U.S. government, along with other potential agents of bioterrorism such as ** [|**Yersinia pestis**]**<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">, Smallpox and Ebola. **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Link to TDR Targets page (if present): **[|**http://www.bindingdb.org/bind/luceneResult.jsp?thisInput=cyclooxygenase-2&submit=Go**]

[|**http://www.ncbi.nlm.nih.gov/protein/3MDL_A**]
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.): **

[|**http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704645/**]
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Essentiality of this protein: **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Target Enzyme: **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Cyclooxygenase ** **<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">(COX), officially known as prostaglandin-endoperoxide synthase (PTGS): **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Why? **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">“ **//**<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Francisella tularensis **//**<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">, a bacterium which causes tularemia in humans, is classified as a CDC category A bioterrorism agent. In this study, we demonstrate that celecoxib, an anti-inflammatory cyclooxygenase-2 inhibitor in clinical use, exhibits activity against a type A strain of //F. tularensis// (Schu S4), the live vaccine strain of //F. tularensis// (a type B strain), and //F. novicida// (“//F. tularensis// subsp. //novicida//”) directly in growth medium. This bacterial killing, however, was not noted with rofecoxib, despite its higher potency than that of celecoxib in inhibiting cyclooxygenase-2. The unique ability of celecoxib to inhibit the proliferation of //F. tularensis// could be pharmacologically exploited to develop novel anti-//Francisella//therapeutic agents, of which the proof of principle is demonstrated by compound 20, a celecoxib derivative identified through the screening of a celecoxib-based focused compound library. Compound 20 inhibited the intracellular proliferation of //Francisella// in macrophages without causing appreciable toxicity to these host cells. Together, these data support the translational potential of compound 20 for the further development of novel, potent anti-//Francisella// agents.” **
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Complex of proteins?: **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): **

[|**http://brenda-enzymes.org/php/result_flat.php4?ecno=1.14.99.1**]
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">See “Essentiality of Protein” section, the target can be drugged/attached to. Also see: **[|**http://www.bindingdb.org/bind/luceneResult.jsp?thisInput=cyclooxygenase-2&submit=Go**]
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">*EC#: ****<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">1.14.99.1 **
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Link to BRENDA EC# page: ****<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Brenda Info: **
 * **<span style="font-family: Arial,sans-serif; font-size: 8pt;">Reaction catalyzed by prostaglandin-endoperoxide synthase (1.14.99.1) **

arachidonate + AH2 + 2 O2 = prostaglandin H2 + A + H2O || ||
 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Image of protein (PyMol with features delineated and shown separately): **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'): **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">Protein Sequence- FASTA: **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">>5COX:A|PDBID|CHAIN|SEQUENCE **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">IMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDP **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">QGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQH **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">LSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">GRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQDPQPTKTA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">TINASASHSRLDDINPTVLIKRRSTEL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">>5COX:B|PDBID|CHAIN|SEQUENCE **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">IMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDP **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">QGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQH **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">LSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">GRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQDPQPTKTA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">TINASASHSRLDDINPTVLIKRRSTEL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">>5COX:C|PDBID|CHAIN|SEQUENCE **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">IMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDP **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">QGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQH **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">LSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">GRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQDPQPTKTA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">TINASASHSRLDDINPTVLIKRRSTEL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">>5COX:D|PDBID|CHAIN|SEQUENCE **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYILTHFKGVWNIVNNIPFLRSL **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">IMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDP **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">QGSNMMFAFFAQHFTHQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHQRVCDILKQEHPEWGDEQLFQTSKLILIGETIKIVIEDYVQH **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">LSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">GRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNNVKGCPFTSFNVQDPQPTKTA **
 * <span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">TINASASHSRLDDINPTVLIKRRSTE **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">*length of your protein in Amino Acids **<span style="font-family: Arial,sans-serif; font-size: 8pt;">: **<span style="color: #00b050; font-family: Arial,sans-serif; font-size: 8pt;">587 **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Weight of Protein: ****<span style="color: #00b050; font-family: Verdana,sans-serif; font-size: 7.5pt;">274398.11 **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): **


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">( ****<span style="color: #008000; font-family: Arial,sans-serif; font-size: 8pt;">link to DNA Works output text file - **<span style="background-color: #ffffff; font-family: Arial,sans-serif; font-size: 8pt;">that should be saved in your <span style="font-family: Arial,sans-serif; font-size: 8pt;"> Google Docs <span style="background-color: #ffffff; font-family: Arial,sans-serif; font-size: 8pt;">folder after you did the primer design protocol)


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Primer design results for 'tail' primers (this is just 2 sequences): **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">**

<span style="background-color: #ffffff; font-family: Arial,sans-serif; font-size: 8pt;">See <span style="font-family: Arial,sans-serif; font-size: 8pt;"> **ProtocolTargetDiscoveryVDS.docx** <span style="background-color: #ffffff; font-family: Arial,sans-serif; font-size: 8pt;">for more
 * <span style="font-family: Arial,sans-serif; font-size: 15.5pt;">Resources: **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">Etiologic Risk Group Categories (for pathogens): http://www.utexas.edu/research/rsc/ibc/agent_class.html#_Toc7238334


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">SIGMA-ALDRICH RESOURCES **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">Enzyme Explorer

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.sigmaaldrich.com/life-science/metabolomics/enzyme-explorer.html

<span style="font-family: Arial,sans-serif; font-size: 8pt;">Enzyme Classification Index (EC number)

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.sigmaaldrich.com/life-science/biochemicals/biochemical-products.html?TablePage=14573088

<span style="font-family: Arial,sans-serif; font-size: 8pt;">WolframAlpha <span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.wolframalpha.com/

<span style="font-family: Arial,sans-serif; font-size: 8pt;">DrugBank <span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.drugbank.ca/


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Databases of genes/organisms: **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.niaid.nih.gov/Pages/default.aspx

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://eupathdb.org/eupathdb/

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@https://patricbrc.vbi.vt.edu/portal/portal/patric/Home

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.nmpdr.org/FIG/wiki/view.cgi/Main/EssentialGenes

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://tubic.tju.edu.cn/deg/

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://csgid.org/csgid/cake/pages/community_request_gateway

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://tdrtargets.org/

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://gsc.jcvi.org/status.shtml


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Scientific Nomenclature page from Center for Disease Control (gene, protein names and abbreviations) **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://wwwnc.cdc.gov/eid/pages/scientific-nomenclature.htm


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Gene Information: **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">NCBI GENE Page: <span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.ncbi.nlm.nih.gov/gene

<span style="font-family: Arial,sans-serif; font-size: 8pt;">BLAST Page: <span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://blast.ncbi.nlm.nih.gov/


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Protein Information: **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">NCBI Protein Page: <span style="font-family: Arial,sans-serif; font-size: 8pt;">@http://www.ncbi.nlm.nih.gov/protein

<span style="font-family: Arial,sans-serif; font-size: 8pt;">Protein Expression Website

<span style="font-family: Arial,sans-serif; font-size: 8pt;">Protein Expression <span style="background-color: #ffffff; font-family: Arial,sans-serif; font-size: 8pt;">Paper: <span style="font-family: Arial,sans-serif; font-size: 8pt;">


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Primer Overlap PCR Articles **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">

<span style="font-family: Arial,sans-serif; font-size: 8pt;">


 * <span style="font-family: Arial,sans-serif; font-size: 8pt;">Is my target good for Virtual Screening programs? **

<span style="font-family: Arial,sans-serif; font-size: 8pt;">