Structure of PDB 7r1t Chain A Binding Site BS01

Receptor Information

>7r1t Chain A (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

MSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQ
LCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSD
LNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGF
FTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNA
SSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSK
FPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVN

Ligand information

• Ligand ID: 6NR
• InChI: InChI=1S/C16H20N6O5S/c17-3-7-4-22(14-10(7)13(19)20-6-21-14)15-12(24)11(23)9(27-15)5-28-2-1-8(18)16(25)26/h4,6,8-9,11-12,15,23-24H,1-2,5,18H2,(H,25,26)(H2,19,20,21)/t8-,9+,11+,12+,15+/m0/s1
• InChIKey: XLTWYAYAFLGUEQ-OPYVMVOTSA-N
• SMILES:
  CACTVS 3.385: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cc(C#N)c3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 2.0.4: c1c(c2c(ncnc2n1C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N)C#N
  CACTVS 3.385: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cc(C#N)c3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 2.0.4: c1c(c2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N)C#N
• Formula: C16 H20 N6 O5 S
• Name: (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid
• ChEMBL: CHEMBL4588797
• ZINC: ZINC000584904932
• PDB chain: 7r1t Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r1t Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): N43 G71 G73 P80 D99 L100 D114 C115 D130 M131 Y132 F149
• Binding residue (residue number reindexed from 1): N44 G72 G74 P81 D100 L101 D115 C116 D131 M132 Y133 F150
• Annotation score: 3

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:7r1t, PDBe:7r1t, PDBj:7r1t
• PDBsum: 7r1t
• PubMed: 36040262
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)