Brand  (β version)

PDB ID: 6WXC

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Ligands
Code Name Style Show Link
CMU 5-chloro-6-(1-(2-iminopyrrolidinyl) methyl) uracil PoSSuM
EDO 1,2-ethanediol PoSSuM
FMT Formic acid PoSSuM
PO4 Phosphate ion PoSSuM
Non-standard Residues
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Structure summary

Code : 6WXC   PDBj   RCSB PDB   PDBe
Header : VIRAL PROTEIN
Title : Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with potential repurposing drug Tipiracil
Release Data : 2020-05-20
Compound :
mol_id molecule chains synonym
1 Uridylate-specific endoribonuclease A,B NSP15 endoribnuclease
ec: 3.1.-.-
Source :
mol_id organism_scientific organism_common expression_system
1 Severe acute respiratory syndrome coronavirus 2  (taxid:2697049) 2019-nCoV Escherichia coli BL21(DE3)  (taxid:469008)
variant: SARS Cov-2
gene: rep, 1a-1b
expression_system_variant: Gold
Authors : Kim, Y., Maltseva, N., Jedrzejczak, R., Welk, L., Endres, M., Chang, C., Michalska, K., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Keywords : SARS Corona virus 2, endoribonuclease, refurbishing drug, COVID-19, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID, VIRAL PROTEIN
Exp. method : X-RAY DIFFRACTION ( 1.85 Å )
Citation :

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.

Kim, Y.,Wower, J.,Maltseva, N.  et al.
(2021)  Commun Biol  4 : 193 - 193

PubMed: 33564093
DOI: 10.1038/s42003-021-01735-9

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Kim, Y.,Wower, J.,Maltseva, N.  et al.
(2020)  Biorxiv 

DOI: 10.1101/2020.06.26.173872

Reaction

Chain : A, B
UniProt : P0DTD1 (R1AB_SARS2)
Reaction: EC: Evidence:
Physiological Direction:
[RNA-directed RNA polymerase nsp12]
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate 		2.7.7.48 PubMed:32358203, PubMed:32438371, PubMed:32526208
-
[Helicase nsp13]
ATP + H2O = ADP + phosphate + H(+) 		3.6.4.12 UniProtKB:P0C6X7
-
[Helicase nsp13]
ATP + H2O = ADP + phosphate + H(+) 		3.6.4.13 UniProtKB:P0C6X7
-
[3C-like proteinase nsp5]
TSAVLQ-|-SGFRK-NH2 and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position. 		3.4.22.69 PubMed:32198291, PubMed:32272481, PubMed:32321856
-
[Papain-like protease nsp3]
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76- residue protein attached to proteins as an intracellular targeting signal). 		3.4.19.12 PubMed:32726803
-
[2'-O-methyltransferase nsp16]
a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'- triphosphoguanosine)-(2'-O-methyl-ribonucleoside) in mRNA + S- adenosyl-L-homocysteine + H(+) 		2.1.1.57 UniProtKB:P0C6X7
-
[Uridylate-specific endoribonuclease nsp15]
uridylyl-uridylyl-ribonucleotide-RNA = a 3'-end uridylyl- 2',3'-cyclophospho-uridine-RNA + a 5'-end dephospho-ribonucleoside- RNA 		- PubMed:33504779, PubMed:33564093
-
[RNA-directed RNA polymerase nsp12]
a 5'-end diphospho-ribonucleoside in mRNA + GTP + H(+) = a 5'- end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate 		2.7.7.50 PubMed:35944563
right-to-left
[Guanine-N7 methyltransferase nsp14]
a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S- adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'- triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- homocysteine 		2.1.1.56 PubMed:35944563
-
Cofactor: Evidence: Note:
Mn(2+) ECO:0000269 | PubMed:33564093
Likely affects Nsp15 binding to RNA.
Mg(2+) ECO:0000269 | PubMed:35944563
Likely affects Nsp15 binding to RNA.