Structure of PDB 6ffs Chain A Binding Site BS01

Receptor Information
>6ffs Chain A (length=182) Species: 12130 (rhinovirus A2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSGPEEEFGMSLIKHNSCVITTENGKFTGLGVYDRFVVVPTHADPGKEIQ
VDGITTKVIDSYDLYNKNGIKLEITVLKLDRNEKFRDIRRYIPNNEDDYP
NCNLALLANQPEPTIINVGDVVSYGNILLSGNQTARMLKYSYPTKSGYCG
GVLYKIGQVLGIHVGGNGRDGFSAMLLRSYFT
Ligand information
Ligand IDD8E
InChIInChI=1S/C26H34FN5O6/c1-16-13-22(31-38-16)26(37)29-20-5-3-4-12-32(2)23(34)11-10-19(15-33)28-25(36)21(30-24(20)35)14-17-6-8-18(27)9-7-17/h6-9,13,19-21,33H,3-5,10-12,14-15H2,1-2H3,(H,28,36)(H,29,37)(H,30,35)/t19-,20-,21-/m0/s1
InChIKeyNMKVYCKPYPCEGS-ACRUOGEOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(no1)C(=O)NC2CCCCN(C(=O)CCC(NC(=O)C(NC2=O)Cc3ccc(cc3)F)CO)C
CACTVS 3.385CN1CCCC[C@H](NC(=O)c2cc(C)on2)C(=O)N[C@@H](Cc3ccc(F)cc3)C(=O)N[C@H](CO)CCC1=O
CACTVS 3.385CN1CCCC[CH](NC(=O)c2cc(C)on2)C(=O)N[CH](Cc3ccc(F)cc3)C(=O)N[CH](CO)CCC1=O
OpenEye OEToolkits 2.0.6Cc1cc(no1)C(=O)N[C@H]2CCCCN(C(=O)CC[C@H](NC(=O)[C@@H](NC2=O)Cc3ccc(cc3)F)CO)C
FormulaC26 H34 F N5 O6
Name~{N}-[(2~{S},5~{S},14~{S})-2-[(4-fluorophenyl)methyl]-5-(hydroxymethyl)-9-methyl-3,8,15-tris(oxidanylidene)-1,4,9-triazacyclopentadec-14-yl]-5-methyl-1,2-oxazole-3-carboxamide;
LIPID FRAGMENT
ChEMBL
DrugBank
ZINC
PDB chain6ffs Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ffs Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors.
Resolution1.86 Å
Binding residue
(original residue number in PDB)		H40 L127 S128 N130 T142 K143 C147 V162 G163 G164 N165 F170
Binding residue
(residue number reindexed from 1)		H42 L129 S130 N132 T144 K145 C149 V164 G165 G166 N167 F172
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.20,IC50=0.063uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6ffs, PDBe:6ffs, PDBj:6ffs
PDBsum6ffs
PubMed29433930
UniProtP04936|POLG_HRV2 Genome polyprotein

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