Structure of PDB 8otr Chain A Binding Site BS02

Receptor Information

>8otr Chain A (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQL
CQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFF
TYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKF
PLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNEN
L

Ligand information

• Ligand ID: W08
• InChI: InChI=1S/C16H23N7O4/c1-22-4-2-8(3-5-22)21-15(26)12-10(24)11(25)16(27-12)23-7-20-9-13(17)18-6-19-14(9)23/h6-8,10-12,16,24-25H,2-5H2,1H3,(H,21,26)(H2,17,18,19)/t10-,11+,12-,16+/m0/s1
• InChIKey: ROJYDYHGBJZLCS-MEQWQQMJSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CN1CCC(CC1)NC(=O)C2C(C(C(O2)n3cnc4c3ncnc4N)O)O
  CACTVS 3.385: CN1CCC(CC1)NC(=O)[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34
  CACTVS 3.385: CN1CCC(CC1)NC(=O)[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
  OpenEye OEToolkits 2.0.7: CN1CCC(CC1)NC(=O)[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
• Formula: C16 H23 N7 O4
• Name: (2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-N-(1-methylpiperidin-4-yl)-3,4-bis(oxidanyl)oxolane-2-carboxamide;
  (2S,3S,4R,5R)-5-(6-Amino-9H-purin-9-yl)-3,4-dihydroxy-N-(1-methyl-4-piperidinyl)tetrahydro-2-furancarboxamide;
  (2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-N-(1-methylpiperidin-4-yl)oxolane-2-carboxamide
• ChEMBL: CHEMBL5282296
• ZINC: ZINC000257299025
• PDB chain: 8otr Chain A Residue 7228

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8otr Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16
• Resolution: 1.77 Å
• Binding residue (original residue number in PDB): D6912 C6913 M6929 D6931 G6946 F6947
• Binding residue (residue number reindexed from 1): D114 C115 M131 D133 G148 F149
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

External links

• PDB: RCSB:8otr, PDBe:8otr, PDBj:8otr
• PDBsum: 8otr
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)