Structure of PDB 7mb2 Chain B Binding Site BS01

Receptor Information

>7mb2 Chain B (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: YVM
• InChI: InChI=1S/C35H43FN4O7/c1-3-19-46-20-17-31(41)39-29(22-25-10-12-27(36)13-11-25)35(45)40-30(21-24-8-6-5-7-9-24)34(44)38-28(14-15-32(42)47-4-2)23-26-16-18-37-33(26)43/h1,5-13,26,28-30H,4,14-23H2,2H3,(H,37,43)(H,38,44)(H,39,41)(H,40,45)/t26-,28+,29+,30-/m0/s1
• InChIKey: AMUUPQIKCDYOIG-XQVPNCLKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccc(cc3)F)NC(=O)CCOCC#C
  CACTVS 3.385: CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)[CH](Cc3ccc(F)cc3)NC(=O)CCOCC#C
  CACTVS 3.385: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccc(F)cc3)NC(=O)CCOCC#C
  ACDLabs 12.01: Fc1ccc(cc1)CC(NC(=O)CCOCC#C)C(=O)NC(Cc1ccccc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC
  OpenEye OEToolkits 2.0.7: CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(Cc3ccc(cc3)F)NC(=O)CCOCC#C
• Formula: C35 H43 F N4 O7
• Name: 4-fluoro-N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide
• PDB chain: 7mb2 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mb2 SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM144
• Resolution: 1.89 Å
• Binding residue (original residue number in PDB): H41 F140 N142 G143 C145 H163 H164 M165 E166 L167 D187 R188 Q189 Q192
• Binding residue (residue number reindexed from 1): H41 F140 N142 G143 C145 H163 H164 M165 E166 L167 D187 R188 Q189 Q192
• 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:7mb2, PDBe:7mb2, PDBj:7mb2
• PDBsum: 7mb2
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)