Structure of PDB 7r7h Chain A Binding Site BS01

Receptor Information

>7r7h Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: 4IT
• InChI: InChI=1S/C23H31N5O4/c1-13(2)9-18(22(30)26-15(12-24)10-14-7-8-25-21(14)29)28-23(31)19-11-16-17(27-19)5-4-6-20(16)32-3/h4-6,11-15,18,24,27H,7-10H2,1-3H3,(H,25,29)(H,26,30)(H,28,31)/b24-12+/t14-,15-,18-/m0/s1
• InChIKey: FFNRAVWDJXOFBV-NGIQPVBXSA-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]3CCNC3=O)C=N
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)C=N
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C=N)NC(=O)c2cc3c([nH]2)cccc3OC
  OpenEye OEToolkits 2.0.7: [H]/N=C/[C@H](CC1CCNC1=O)NC(=O)[C@H](CC(C)C)NC(=O)c2cc3c([nH]2)cccc3OC
  ACDLabs 12.01: COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C=N
• Formula: C23 H31 N5 O4
• Name: N-[(2S)-1-({(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
• PDB chain: 7r7h Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r7h Peptidomimetic nitrile warheads as SARS-CoV-2 3CL protease inhibitors.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 P168 D187 Q189 T190
• Binding residue (residue number reindexed from 1): H41 F140 N142 C145 H163 H164 M165 E166 P168 D187 Q189 T190
• 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:7r7h, PDBe:7r7h, PDBj:7r7h
• PDBsum: 7r7h
• PubMed: 34778773
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)