Structure of PDB 8ov2 Chain A Binding Site BS01

Receptor Information

>8ov2 Chain A (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQL
CQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFF
TYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKF
PLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNEN
L

Ligand information

• Ligand ID: SGV
• InChI: InChI=1S/C12H15N5O5/c13-9-6-4(10(14)21)1-17(11(6)16-3-15-9)12-8(20)7(19)5(2-18)22-12/h1,3,5,7-8,12,18-20H,2H2,(H2,14,21)(H2,13,15,16)/t5-,7-,8-,12-/m1/s1
• InChIKey: OBZJZDHRXBKKTJ-JTFADIMSSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)C(=O)N
  ACDLabs 12.01: O=C(c2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N)N
  CACTVS 3.370: NC(=O)c1cn([CH]2O[CH](CO)[CH](O)[CH]2O)c3ncnc(N)c13
  OpenEye OEToolkits 1.7.0: c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N)C(=O)N
  CACTVS 3.370: NC(=O)c1cn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c3ncnc(N)c13
• Formula: C12 H15 N5 O5
• Name: SANGIVAMYCIN;
  4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide
• ChEMBL: CHEMBL101892
• ZINC: ZINC000004217438
• PDB chain: 8ov2 Chain A Residue 7222

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ov2 Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16
• Resolution: 1.86 Å
• Binding residue (original residue number in PDB): D6897 L6898 D6912 C6913 M6929 Y6930 F6947
• Binding residue (residue number reindexed from 1): D99 L100 D114 C115 M131 Y132 F149
• Annotation score: 1

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:8ov2, PDBe:8ov2, PDBj:8ov2
• PDBsum: 8ov2
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)