Structure of PDB 8rv7 Chain A Binding Site BS01

Receptor Information

>8rv7 Chain A (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQL
CQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFF
TYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKF
PLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN

Ligand information

• Ligand ID: A1H3E
• InChI: InChI=1S/C21H23N5O6S/c22-18-15-19(24-9-23-18)26(10-25-15)20-17(29)16(28)14(32-20)8-33-7-12-4-11(2-1-3-27)5-13(6-12)21(30)31/h1-2,4-6,9-10,14,16-17,20,27-29H,3,7-8H2,(H,30,31)(H2,22,23,24)/b2-1+/t14-,16-,17-,20-/m1/s1
• InChIKey: HVLWKBDZYHPIQO-FEIMRTCESA-N
• SMILES:
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](CSCc4cc(C=CCO)cc(c4)C(O)=O)[CH](O)[CH]3O
  OpenEye OEToolkits 2.0.7: c1c(cc(cc1/C=C/CO)C(=O)O)CSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O
  OpenEye OEToolkits 2.0.7: c1c(cc(cc1C=CCO)C(=O)O)CSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCc4cc(\C=C\CO)cc(c4)C(O)=O)[C@@H](O)[C@H]3O
• Formula: C21 H23 N5 O6 S
• Name: 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(3-oxidanylprop-1-ynyl)benzoic acid
• PDB chain: 8rv7 Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rv7 SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 4
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G71 D99 L100 C115 M131 Y132 P134
• Binding residue (residue number reindexed from 1): G71 D99 L100 C115 M131 Y132 P134
• 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:8rv7, PDBe:8rv7, PDBj:8rv7
• PDBsum: 8rv7
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)