Structure of PDB 8otr Chain A Binding Site BS01

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: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 8otr Chain A Residue 7213

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): N6841 G6869 G6871 G6879 D6897 L6898 C6913 D6928 M6929 Y6930 K6968
• Binding residue (residue number reindexed from 1): N43 G71 G73 G81 D99 L100 C115 D130 M131 Y132 K170
• Annotation score: 5

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)