Structure of PDB 8u3o Chain A Binding Site BS01

Receptor Information

>8u3o Chain A (length=297) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

RKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPN
YEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKF
VRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNID
YDCVSFCYMHHMELPTGVHVGTDLEGNFYGPFVDRQTAQAAGTDTTITVN
VLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPL
SAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: O69
• InChI: InChI=1S/C35H31N5O2/c1-21(23-15-14-22-8-3-4-9-24(22)16-23)38-35(42)29-12-7-13-31-32(29)40(27-17-26(18-27)34(41)36-2)33(39-31)30-20-37-19-25-10-5-6-11-28(25)30/h3-16,19-21,26-27H,17-18H2,1-2H3,(H,36,41)(H,38,42)/t21-,26-,27+/m0/s1
• InChIKey: YXZCMQAWBHCPMS-NJTBCWBZSA-N
• SMILES:
  CACTVS 3.385: CNC(=O)[C@@H]1C[C@@H](C1)n2c(nc3cccc(C(=O)N[C@@H](C)c4ccc5ccccc5c4)c23)c6cncc7ccccc67
  OpenEye OEToolkits 2.0.7: CC(c1ccc2ccccc2c1)NC(=O)c3cccc4c3n(c(n4)c5cncc6c5cccc6)C7CC(C7)C(=O)NC
  OpenEye OEToolkits 2.0.7: C[C@@H](c1ccc2ccccc2c1)NC(=O)c3cccc4c3n(c(n4)c5cncc6c5cccc6)C7CC(C7)C(=O)NC
  CACTVS 3.385: CNC(=O)[CH]1C[CH](C1)n2c(nc3cccc(C(=O)N[CH](C)c4ccc5ccccc5c4)c23)c6cncc7ccccc67
  ACDLabs 12.01: CNC(=O)C1CC(C1)n1c2c(cccc2nc1c1cncc2ccccc21)C(=O)NC(C)c1cc2ccccc2cc1
• Formula: C35 H31 N5 O2
• Name: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide
• PDB chain: 8u3o Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8u3o SARS-CoV-2 Main Protease A173V in complex with CDD-1819
• Resolution: 1.88 Å
• Binding residue (original residue number in PDB): T25 T26 M49 F140 L141 N142 G143 S144 C145 H163 M165 E166 R188
• Binding residue (residue number reindexed from 1): T22 T23 M46 F137 L138 N139 G140 S141 C142 H160 M162 E163 R185
• Annotation score: 1

External links

• PDB: RCSB:8u3o, PDBe:8u3o, PDBj:8u3o
• PDBsum: 8u3o
• UniProt: A0A7U3H5H9