Structure of PDB 5rh0 Chain A Binding Site BS01

Receptor Information

>5rh0 Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: UH4
• InChI: InChI=1S/C11H11N3OS/c1-8-4-5-10(16-8)14-11(15)13-9-3-2-6-12-7-9/h2-7H,1H3,(H2,13,14,15)
• InChIKey: OCXJDZBTSLHCNX-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1ccc(s1)NC(=O)Nc2cccnc2
  ACDLabs 12.01: N(C(Nc1ccc(s1)C)=O)c2cccnc2
  CACTVS 3.385: Cc1sc(NC(=O)Nc2cccnc2)cc1
• Formula: C11 H11 N3 O S
• Name: N-(5-methylthiophen-2-yl)-N'-pyridin-3-ylurea
• PDB chain: 5rh0 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5rh0 PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen
• Resolution: 1.916 Å
• Binding residue (original residue number in PDB): M49 F140 L141 N142 C145 H163 M165 E166 R188 Q189
• Binding residue (residue number reindexed from 1): M49 F140 L141 N142 C145 H163 M165 E166 R188 Q189
• 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:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:5rh0, PDBe:5rh0, PDBj:5rh0
• PDBsum: 5rh0
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)