Structure of PDB 7lcr Chain B Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: XTM
• InChI: InChI=1S/C21H30FN3O5/c1-13(2)8-18(25-21(29)30-12-14-4-3-5-16(22)9-14)20(28)24-17(11-26)10-15-6-7-23-19(15)27/h3-5,9,13,15,17-18,26H,6-8,10-12H2,1-2H3,(H,23,27)(H,24,28)(H,25,29)/t15-,17-,18-/m0/s1
• InChIKey: KSFOLLAEZGAOFV-SZMVWBNQSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)CO)NC(=O)OCc2cccc(c2)F
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1cccc(F)c1)C(=O)N[CH](CO)C[CH]2CCNC2=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1cccc(F)c1)C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)CO)NC(=O)OCc2cccc(c2)F
  ACDLabs 12.01: C2(=O)C(CC(NC(C(CC(C)C)NC(OCc1cccc(F)c1)=O)=O)CO)CCN2
• Formula: C21 H30 F N3 O5
• Name: N~2~-{[(3-fluorophenyl)methoxy]carbonyl}-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
• PDB chain: 7lcr Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lcr Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): F140 G143 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): F140 G143 C145 H163 H164 M165 E166 D187 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:7lcr, PDBe:7lcr, PDBj:7lcr
• PDBsum: 7lcr
• PubMed: 34118724
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)