Structure of PDB 2qiq Chain A Binding Site BS01

Receptor Information
>2qiq Chain A (length=301) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDML
NPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTI
TLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQC
S
Ligand information
Ligand IDCYV
InChIInChI=1S/C32H54N4O9/c1-9-44-26(39)13-12-23(16-22-14-15-33-28(22)40)34-29(41)21(11-10-19(2)3)17-25(38)27(20(4)5)36-30(42)24(18-37)35-31(43)45-32(6,7)8/h10,20-24,27,37H,9,11-18H2,1-8H3,(H,33,40)(H,34,41)(H,35,43)(H,36,42)/t21-,22-,23-,24+,27+/m1/s1
InChIKeyCSVHTXSZRNRRSB-AHPXAKOISA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC=C(C)C)CC(=O)[CH](NC(=O)[CH](CO)NC(=O)OC(C)(C)C)C(C)C
CACTVS 3.341CCOC(=O)CC[C@H](C[C@H]1CCNC1=O)NC(=O)[C@H](CC=C(C)C)CC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)OC(C)(C)C)C(C)C
OpenEye OEToolkits 1.5.0CCOC(=O)CC[C@H](C[C@H]1CCNC1=O)NC(=O)[C@H](CC=C(C)C)CC(=O)[C@H](C(C)C)NC(=O)[C@H](CO)NC(=O)OC(C)(C)C
OpenEye OEToolkits 1.5.0CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(CC=C(C)C)CC(=O)C(C(C)C)NC(=O)C(CO)NC(=O)OC(C)(C)C
ACDLabs 10.04O=C(OC(C)(C)C)NC(C(=O)NC(C(=O)CC(C(=O)NC(CC1C(=O)NCC1)CCC(=O)OCC)C\C=C(/C)C)C(C)C)CO
FormulaC32 H54 N4 O9
NameETHYL (4R)-4-{[(2R,5S)-5-{[N-(TERT-BUTOXYCARBONYL)-L-SERYL]AMINO}-6-METHYL-2-(3-METHYLBUT-2-EN-1-YL)-4-OXOHEPTANOYL]AMINO}-5-[(3R)-2-OXOPYRROLIDIN-3-YL]PENTANOATE
ChEMBL
DrugBank
ZINCZINC000037868584
PDB chain2qiq Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2qiq Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		T26 H41 F140 L141 N142 C145 H163 H164 M165 E166 P168 D187 Q189 T190 Q192
Binding residue
(residue number reindexed from 1)		T26 H41 F140 L141 N142 C145 H163 H164 M165 E166 P168 D187 Q189 T190 Q192
Annotation score1
Binding affinityMOAD: ic50=80uM
PDBbind-CN: -logKd/Ki=4.10,IC50=80uM
BindingDB: IC50=80000nM
Enzymatic activity
Catalytic site (original residue number in PDB) H41 G143 C145
Catalytic site (residue number reindexed from 1) H41 G143 C145
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2qiq, PDBe:2qiq, PDBj:2qiq
PDBsum2qiq
PubMed17855091
UniProtP0C6X7|R1AB_SARS Replicase polyprotein 1ab (Gene Name=rep)

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