Structure of PDB 7mb3 Chain A Binding Site BS01

Receptor Information

>7mb3 Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: YVV
• InChI: InChI=1S/C35H44N4O7/c1-3-20-45-21-18-31(40)38-29(22-25-11-7-5-8-12-25)35(44)39-30(23-26-13-9-6-10-14-26)34(43)37-28(15-16-32(41)46-4-2)24-27-17-19-36-33(27)42/h1,5-14,27-30H,4,15-24H2,2H3,(H,36,42)(H,37,43)(H,38,40)(H,39,44)/t27-,28+,29+,30-/m0/s1
• InChIKey: DFVBMNVNJFHZTI-KJHMZRPRSA-N
• SMILES:
  CACTVS 3.385
  OpenEye OEToolkits 2.0.7: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccccc3)NC(=O)CCOCC#C
  OpenEye OEToolkits 2.0.7: CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(Cc3ccccc3)NC(=O)CCOCC#C
  ACDLabs 12.01: C#CCOCCC(=O)NC(Cc1ccccc1)C(=O)NC(Cc1ccccc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC
  CACTVS 3.385: CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)[CH](Cc3ccccc3)NC(=O)CCOCC#C
• Formula: C35 H44 N4 O7
• Name: 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: 7mb3 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mb3 SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM145
• Resolution: 1.81 Å
• Binding residue (original residue number in PDB): H41 F140 N142 G143 S144 C145 H163 H164 M165 E166 P168 D187 R188 Q189 T190 A191
• Binding residue (residue number reindexed from 1): H41 F140 N142 G143 S144 C145 H163 H164 M165 E166 P168 D187 R188 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:7mb3, PDBe:7mb3, PDBj:7mb3
• PDBsum: 7mb3
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)