Structure of PDB 7maw Chain B Binding Site BS01

Receptor Information

>7maw Chain B (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: YVA
• InChI: InChI=1S/C28H35N3O5/c1-3-19-5-7-20(8-6-19)11-13-25(32)31-24(17-21-9-10-21)28(35)30-23(12-14-26(33)36-4-2)18-22-15-16-29-27(22)34/h1,5-8,11,13,21-24H,4,9-10,12,14-18H2,2H3,(H,29,34)(H,30,35)(H,31,32)/b13-11+/t22-,23+,24-/m0/s1
• InChIKey: JMWBRPAKKKBHFQ-NQRMBFEXSA-N
• SMILES:
  CACTVS 3.385: CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC2CC2)NC(=O)C=Cc3ccc(cc3)C#C
  ACDLabs 12.01: C#Cc1ccc(cc1)/C=C/C(=O)NC(CC1CC1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC
  OpenEye OEToolkits 2.0.7: CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(CC2CC2)NC(=O)C=Cc3ccc(cc3)C#C
  CACTVS 3.385: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)\C=C\c3ccc(cc3)C#C
  OpenEye OEToolkits 2.0.7: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)/C=C/c3ccc(cc3)C#C
• Formula: C28 H35 N3 O5
• Name: ethyl (4R)-4-({3-cyclopropyl-N-[(2E)-3-(4-ethynylphenyl)prop-2-enoyl]-L-alanyl}amino)-5-[(3S)-2-oxopyrrolidin-3-yl]pentanoate
• PDB chain: 7maw Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7maw SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM129
• Resolution: 2.07 Å
• Binding residue (original residue number in PDB): T26 H41 F140 N142 G143 C145 H164 M165 E166 D187 T190 A191
• Binding residue (residue number reindexed from 1): T26 H41 F140 N142 G143 C145 H164 M165 E166 D187 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:7maw, PDBe:7maw, PDBj:7maw
• PDBsum: 7maw
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)