Structure of PDB 6wco Chain A Binding Site BS01

Receptor Information
>6wco Chain A (length=306) Species: 228330 (SARS coronavirus Urbani) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDML
NPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTI
TLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
SGVTFQ
Ligand information
Ligand IDX47
InChIInChI=1S/C26H31N5O2/c1-26(2,3)19-10-12-21(13-11-19)31(25(33)22-16-28-17-29-22)23(18-7-6-14-27-15-18)24(32)30-20-8-4-5-9-20/h6-7,10-17,20,23H,4-5,8-9H2,1-3H3,(H,28,29)(H,30,32)/t23-/m1/s1
InChIKeyGYSUWMLOWVCSQJ-HSZRJFAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N([C@H](c2cccnc2)C(=O)NC3CCCC3)C(=O)c4c[nH]cn4
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([C@@H](C(=O)NC2CCCC2)c3cccnc3)C(=O)c4c[nH]cn4
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N(C(c2cccnc2)C(=O)NC3CCCC3)C(=O)c4c[nH]cn4
ACDLabs 12.01C(=O)(c1ncnc1)N(c2ccc(C(C)(C)C)cc2)C(c3cccnc3)C(NC4CCCC4)=O
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([CH](C(=O)NC2CCCC2)c3cccnc3)C(=O)c4c[nH]cn4
FormulaC26 H31 N5 O2
NameN-(4-tert-butylphenyl)-N-[(1R)-2-(cyclopentylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain6wco Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wco A taxonomically-driven approach to development of potent, broad-spectrum inhibitors of coronavirus main protease including SARS-CoV-2 (COVID-19)
Resolution1.48 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 Q189
Annotation score1
Binding affinityBindingDB: IC50=1700nM
Enzymatic activity
Enzyme Commision number 2.1.1.-
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

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Molecular Function

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Biological Process
External links
PDB RCSB:6wco, PDBe:6wco, PDBj:6wco
PDBsum6wco
PubMed
UniProtP0C6X7|R1AB_SARS Replicase polyprotein 1ab (Gene Name=rep)

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