Structure of PDB 7maz Chain B Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: YVD
• InChI: InChI=1S/C29H36F2N4O5/c1-2-40-26(36)12-11-23(17-20-13-14-33-27(20)37)34-29(39)25(16-19-5-9-22(31)10-6-19)35-28(38)24(32)15-18-3-7-21(30)8-4-18/h3-10,20,23-25H,2,11-17,32H2,1H3,(H,33,37)(H,34,39)(H,35,38)/t20-,23+,24+,25-/m0/s1
• InChIKey: WOTTZMBQRDTTCI-KTJVCJKDSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccc(cc2)F)NC(=O)C(Cc3ccc(cc3)F)N
  CACTVS 3.385: CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccc(F)cc2)NC(=O)[CH](N)Cc3ccc(F)cc3
  ACDLabs 12.01: Fc1ccc(cc1)CC(N)C(=O)NC(Cc1ccc(F)cc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC
  OpenEye OEToolkits 2.0.7: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccc(cc2)F)NC(=O)[C@@H](Cc3ccc(cc3)F)N
  CACTVS 3.385: CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccc(F)cc2)NC(=O)[C@H](N)Cc3ccc(F)cc3
• Formula: C29 H36 F2 N4 O5
• Name: 4-fluoro-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-4-fluoro-L-phenylalaninamide
• PDB chain: 7maz Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7maz SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor SM139
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 D187 R188 Q189 Q192
• Binding residue (residue number reindexed from 1): H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 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:7maz, PDBe:7maz, PDBj:7maz
• PDBsum: 7maz
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)