IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. The Journal of biological chemistry 2015 imex curation Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. amesecar@purdue.edu Only protein-protein interactions imex curation in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. amesecar@purdue.edu Accepted 2020-JUN-11 AT 14:03 BST AT 14:03 BST by MARTA The Journal of biological chemistry 2015 Only protein-protein interactions imex curation imex curation Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. The Journal of biological chemistry 2015 imex curation Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. amesecar@purdue.edu Only protein-protein interactions imex curation in vitro In vitro protease assay protease assay predetermined predetermined participant predetermined Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. The rate of enzymatic activity was determined at 25 deg.C by following the increase in fluorescence of Hilyte FluorTM-488 upon peptide hydrolysis by the enzyme. amesecar@purdue.edu Accepted 2020-JUN-11 AT 14:03 BST AT 14:03 BST by MARTA The Journal of biological chemistry 2015 Only protein-protein interactions imex curation imex curation Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. The Journal of biological chemistry 2015 imex curation Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins Coronavirus - Interactions investigated in the context of Coronavirus This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. amesecar@purdue.edu Only protein-protein interactions imex curation in vitro In vitro solution sedimentati cosedimentation in solution solution sedimentati predetermined predetermined participant predetermined Tomar S., Johnston ML., St John SE., Osswald HL., Nyalapatla PR., Paul LN., Ghosh AK., Denison MR., Mesecar AD. Virus - Publications including interactions involving viral proteins This publication is curated for benefit of Birgit - evidence for complex for NSP5 (MERS). Thus I have only created Chebi entries for compounds 6, 10 and 11 as Chebi complain if we create too many unnecessary molecules and other inhibitor compounds only have results quoted in Table 3. amesecar@purdue.edu Accepted 2020-JUN-11 AT 14:03 BST AT 14:03 BST by MARTA The Journal of biological chemistry 2015 Only protein-protein interactions imex curation imex curation p0c6x7-pro_0000037312 3C-like proteinase nsp5 rep ORF1ab polyprotein 1a-1b protein protein sars-cov Human SARS coronavirus SARS-CoV Severe acute respiratory syndrome coronavirus SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ 3241 3546 8A3486F9E1A9A89D generic peptide substrate peptide peptide polypeptide oligopeptide oligopeptide polypeptide chemical synthesis Chemical synthesis (Chemical synthesis) ESATLQSGLRKAK k9n7c7-pro_0000422443 3C-like proteinase rep ORF1ab polyprotein 1a-1b protein protein cvemc Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012) (Betacoronavirus England 1) Betacoronavirus England 1 Human coronavirus EMC SGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQLSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVANPSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMGVVMQ 3248 3553 F539287F641722AE compound number 6 compound number 6 small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) compound 10 compound 10 small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) compound number 11 compound number 11 small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) p0c6w3-pro_0000290292 3C-like proteinase rep ORF1ab polyprotein 1a-1b protein protein BtCoV Bat coronavirus HKU4 BtCoV/HKU4/2004 SGLVKMSAPSGAVENCIVQVTCGSMTLNGLWLDNTVWCPRHIMCPADQLTDPNYDALLISKTNHSFIVQKHIGAQANLRVVAHSMVGVLLKLTVDVANPSTPAYTFSTVKPGASFSVLACYNGKPTGVFTVNLRHNSTIKGSFLCGSCGSVGYTENGGVINFVYMHQMELSNGTHTGSSFDGVMYGAFEDKQTHQLQLTDKYCTINVVAWLYAAVLNGCKWFVKPTRVGIVTYNEWALSNQFTEFVGTQSIDMLAHRTGVSVEQMLAAIQSLHAGFQGKTILGQSTLEDEFTPDDVNMQVMGVVMQ 3292 3597 97E5545B56C6C139 p0c6w4-pro_0000290307 3C-like proteinase rep ORF1ab polyprotein 1a-1b protein protein BtCoV-1 Bat coronavirus HKU5 BtCoV/HKU5/2004 SGLVKMAAPSGVVENCMVQVTCGSMTLNGLWLDNYVWCPRHVMCPADQLSDPNYDALLVSKTNLSFIVQKNVGAPANLRVVGHTMVGTLLKLTVESANPQTPAYTFTTVKPGASFSVLACYNGRPTGVFMVNMRQNSTIKGSFLCGSCGSVGYTQEGNVINFCYMHQMELSNGTHTGCAFDGVMYGAFEDRQVHQVQLSDKYCTINIVAWLYAAILNGCNWFVKPNKTGIATFNEWAMSNQFTEFIGTQSVDMLAHKTGVSVEQLLYAIQTLHKGFQGKTILGNSMLEDEFTPDDVNMQVMGVVMQ 3339 3644 015ACFBB044D84C4 compound number 6-rep-1 1 7 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component purified purified S-hydroxy-L-cysteine cysoh L-cysteine sulfenic acid (2R)-2-amino-3-(hydroxysulfanyl)propanoic acid (2R)-2-amino-3-(oxido-lambda(4)-sulfanyl)propanoic acid [tautomer] 2-amino-2-carboxyethanesulfenic acid 2-amino-3-sulfinylpropanoic acid [tautomer] 3-sulfenoalanine ACT_SITE Cysteine sulfenic acid (-SOH) intermediate L-cysteine sulfenic acid MOD_RES Cysteine sulfenic acid (-SOH) S-hydroxycysteine S-oxocysteine [tautomer] S-oxycysteine [tautomer] cysteine S-oxide [tautomer] cysteine sulfoxide [tautomer] cysteine sulphenic acid CysOH Oxidation Sulfenic Acid (from Cysteine) mod193 certain certain sequence position certain certain certain sequence position certain ecoli Escherichia coli (strain K12) direct interaction direct interaction Table 4 I do not trust the PDBe entry for this one - they use a Trembl entry which has same sequence as SwissP entry, no mention of compound 6, and I think the peptide XSVLX is meant to be the other molecule of NSP5 as the SVL sequence is found in NSP5. compound number 11-rep-1 1 9 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction table 4 generic peptide substrate-rep-1 2 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 6 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage 1A/B, 2, number 1, figure 3, 5A The enzymatic efficiency of MERS-CoV 3CLpro (kcat/Km = 3.1 ± 0.03 × 10E2 /um /min) is noticeably lower than other 3CLpro enzymes tested. The response of MERS-CoV 3CLpro enzymatic activity to an increasing enzyme concentration is nonlinear. There is a substantial reduction in the ability of MERS-CoV 3CLpro to dimerize compared with the other 3CLpro enzymes. generic peptide substrate-rep-2 2 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 4 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage 1A/B, 2, number 2 kcat/Km =15.5 × 10E2 /um /min) generic peptide substrate-rep-3 2 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 11 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage 1A/B, 2, number 3 kcat/Km =8.8 × 10E2 /um /min) generic peptide substrate-rep-4 2 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 10 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage 1A/B, 2, number 4 kcat/Km =11.3 × 10E2 /um /min) generic peptide substrate-rep-5 2 7 inhibitor inhibitor neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 6 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage Figure 3, Table 3 compound number 6-generic peptide substrate-1 2 7 inhibitor inhibitor neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 11 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage text only, HKU5 compound number 6-generic peptide substrate-2 2 7 inhibitor inhibitor neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 10 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage text only, HKU4 rep-90 3 6 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 4A The dimer peak becoming more pronounced at higher enzyme concentrations. Compound 6 -CHEBI:149679 Compound 10 -CHEBI:149693 rep-89 3 7 stimulator stimulator neutral component neutral component unknown region binding region binding-associated region binding region undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component purified purified active site cysteine cys L-cysteine residue (2R)-2-amino-3-sulfanylpropanoic acid (R)-cysteine 2-amino-3-mercaptopropanoic acid 2-amino-3-mercaptopropionic acid 2-azanyl-3-sulfanylpropanoic acid 3-mercapto-L-alanine L-(+)-cysteine L-cysteine alpha-amino-beta-mercaptopropanoic acid alpha-amino-beta-mercaptopropionic acid alpha-amino-beta-thiolpropionic acid beta-mercaptoalanine half-cystine thioserine Cys Cysteine (C, Cys) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined ecoli Escherichia coli (strain K12) 61 63 covalent binding covalent binding 4B compound 10-generic peptide substrate-1 2 8 inhibitor inhibitor neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 5 enzyme target enzyme target substrate substrate neutral component neutral component purified purified C-terminus qx 520 qx 520 c-term range C-terminal range c-term range c-term range C-terminal range c-term range n-terminus hilyte 488 hilyte fluor 488 hilyte 488 n-term range n-terminal range n-term range n-term range n-terminal range n-term range chemical synthesis Chemical synthesis (Chemical synthesis) 6 enzyme enzyme neutral component neutral component purified purified ecoli Escherichia coli (strain K12) protein cleavage protein cleavage Table 3, figure 5A Ki=>100uM. Data from Table 3 derived from these experimentaal conditions: incubation of 500 nm MERS-CoV 3CLpro with 50 um of compound 10. cannot enter a Ki of ">" anything as a Parameter. An increase in the activity of MERS-CoV 3CLpro, as high as 195%, was observed in the presence of low inhibitor concentrations (0.1 to 20 um). Inhibition of enzymatic activity was observed only at higher inhibitor concentrations (40 um or greater). compound number 6-rep-2 3 8 stimulator stimulator neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) 6 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction 4C