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Structure of PDB 6xmk Chain A Binding Site BS01

Receptor Information

>6xmk Chain A (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

RKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPN
YEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKF
VRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNID
YDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVN
VLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPL
SAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: QYS
• InChI: InChI=1S/C21H35F2N3O8S/c1-12(2)9-15(26-20(30)34-11-13-3-6-21(22,23)7-4-13)18(28)25-16(19(29)35(31,32)33)10-14-5-8-24-17(14)27/h12-16,19,29H,3-11H2,1-2H3,(H,24,27)(H,25,28)(H,26,30)(H,31,32,33)/t14-,15-,16-,19?/m0/s1
• InChIKey: BHZBRFONZANPNK-ZYHFAYPJSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(CC2)(F)F
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC2CCC(CC2)(F)F
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCC1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
  ACDLabs 12.01: C2(F)(CCC(COC(=O)NC(CC(C)C)C(NC(CC1C(=O)NCC1)C(S(=O)(=O)O)O)=O)CC2)F
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCC1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
• Formula: C21 H35 F2 N3 O8 S
• Name: (1S,2S)-2-[(N-{[(4,4-difluorocyclohexyl)methoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• ChEMBL: CHEMBL5095608
• PDB chain: 6xmk Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xmk 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F140 N142 G143 C145 H163 H164 M165 E166 Q189 A191
• Binding residue (residue number reindexed from 1): F137 N139 G140 C142 H160 H161 M162 E163 Q186 A188
• Annotation score: 1
• Binding affinity: BindingDB: IC50=450nM

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:6xmk, PDBe:6xmk, PDBj:6xmk
• PDBsum: 6xmk
• PubMed: 32747425
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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