Structure of PDB 7mbi Chain D Binding Site BS01

Receptor Information

>7mbi Chain D (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: YWJ
• InChI: InChI=1S/C25H34N4O5/c1-14(2)11-20(24(32)28-19(15(3)30)12-16-7-6-10-26-23(16)31)29-25(33)21-13-17-18(27-21)8-5-9-22(17)34-4/h5,8-9,13-14,16,19-20,27H,6-7,10-12H2,1-4H3,(H,26,31)(H,28,32)(H,29,33)/t16-,19-,20-/m0/s1
• InChIKey: HDPZWFCIPQRUTJ-VDGAXYAQSA-N
• SMILES:
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCCNC3=O)C(C)=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCCNC1=O)C(=O)C)NC(=O)c2cc3c([nH]2)cccc3OC
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCCNC1=O)C(=O)C)NC(=O)c2cc3c([nH]2)cccc3OC
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCCNC3=O)C(C)=O
  ACDLabs 12.01: COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCCNC1=O)C(C)=O
• Formula: C25 H34 N4 O5
• Name: 4-methoxy-N-[(2S)-4-methyl-1-oxo-1-({(2S)-3-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}amino)pentan-2-yl]-1H-indole-2-carboxamide
• PDB chain: 7mbi Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mbi Peptidomimetic alpha-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): H41 F140 C145 H163 H164 M165 E166 Q189 T190 A191
• Binding residue (residue number reindexed from 1): H41 F140 C145 H163 H164 M165 E166 Q189 T190 A191
• 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:7mbi, PDBe:7mbi, PDBj:7mbi
• PDBsum: 7mbi
• PubMed: 34242027
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)