Structure of PDB 7ldl Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: XV4
• InChI: InChI=1S/C23H32N4O5/c1-13(2)9-18(22(30)25-15(12-28)10-14-7-8-24-21(14)29)27-23(31)19-11-16-17(26-19)5-4-6-20(16)32-3/h4-6,11,13-15,18,26,28H,7-10,12H2,1-3H3,(H,24,29)(H,25,30)(H,27,31)/t14-,15-,18-/m0/s1
• InChIKey: WHTWOUANZWYZGR-MPGHIAIKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)CO)NC(=O)c2cc3c([nH]2)cccc3OC
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)CO)NC(=O)c2cc3c([nH]2)cccc3OC
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](CO)C[CH]3CCNC3=O
  CACTVS 3.385: COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O
  ACDLabs 12.01: C3(C(CC(NC(C(CC(C)C)NC(c1nc2c(c1)c(OC)ccc2)=O)=O)CO)CCN3)=O
• Formula: C23 H32 N4 O5
• Name: N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
• PDB chain: 7ldl Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ldl Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 D187 Q189 T190 A191
• Binding residue (residue number reindexed from 1): H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 D187 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:7ldl, PDBe:7ldl, PDBj:7ldl
• PDBsum: 7ldl
• PubMed: 34118724
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)