Structure of PDB 6ffn Chain A Binding Site BS01

Receptor Information

>6ffn Chain A (length=182) Species: 12130 (rhinovirus A2)

GSGPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQ
VDGITTKVIDSYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYP
NCNLALLANQPEPTIINVGDVVSYGNILLSGNQTARMLKYSYPTKSGYCG
GVLYKIGQVLGIHVGGNGRDGFSAMLLRSYFT

Ligand information

• Ligand ID: D8K
• InChI: InChI=1S/C27H33FN6O7/c1-15-11-20(33-41-15)25(38)32-21-13-29-27(40)22-3-2-10-34(22)23(36)9-8-18(14-35)30-24(37)19(31-26(21)39)12-16-4-6-17(28)7-5-16/h4-7,11,18-19,21-22,35H,2-3,8-10,12-14H2,1H3,(H,29,40)(H,30,37)(H,31,39)(H,32,38)/t18-,19-,21-,22+/m0/s1
• InChIKey: XGIISLQJIYRWPH-BLKABHOGSA-N
• SMILES:
  CACTVS 3.385: Cc1onc(c1)C(=O)N[CH]2CNC(=O)[CH]3CCCN3C(=O)CC[CH](CO)NC(=O)[CH](Cc4ccc(F)cc4)NC2=O
  CACTVS 3.385: Cc1onc(c1)C(=O)N[C@H]2CNC(=O)[C@H]3CCCN3C(=O)CC[C@@H](CO)NC(=O)[C@H](Cc4ccc(F)cc4)NC2=O
  OpenEye OEToolkits 2.0.6: Cc1cc(no1)C(=O)N[C@H]2CNC(=O)[C@H]3CCCN3C(=O)CC[C@H](NC(=O)[C@@H](NC2=O)Cc4ccc(cc4)F)CO
  OpenEye OEToolkits 2.0.6: Cc1cc(no1)C(=O)NC2CNC(=O)C3CCCN3C(=O)CCC(NC(=O)C(NC2=O)Cc4ccc(cc4)F)CO
• Formula: C27 H33 F N6 O7
• Name: ~{N}-[(5~{S},8~{S},11~{S},15~{R})-8-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-2,7,10,14-tetrakis(oxidanylidene)-1,6,9,13-tetrazabicyclo[13.3.0]octadecan-11-yl]-5-methyl-1,2-oxazole-3-carboxamide
• PDB chain: 6ffn Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ffn Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): H40 E71 L127 S128 N130 T142 C147 V162 G163 G164 N165 G166 F170
• Binding residue (residue number reindexed from 1): H42 E73 L129 S130 N132 T144 C149 V164 G165 G166 N167 G168 F172
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.22,IC50=0.006uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H40 E71 G145 C147
• Catalytic site (residue number reindexed from 1): H42 E73 G147 C149
• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.22.28: picornain 3C.
  3.4.22.29: picornain 2A.
  3.6.1.15: nucleoside-triphosphate phosphatase.

Gene Ontology

Molecular Function

• GO:0004197 cysteine-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:6ffn, PDBe:6ffn, PDBj:6ffn
• PDBsum: 6ffn
• PubMed: 29433930
• UniProt: P04936|POLG_HRV2 Genome polyprotein