Structure of PDB 7jkv Chain B Binding Site BS01

Receptor Information
>7jkv Chain B (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM
LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTP
KYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVG
FNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTT
ITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDI
LGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ
CS
Ligand information
Ligand IDV7G
InChIInChI=1S/C30H35N5O5S/c1-16(2)13-22(34-29(39)23-15-18-19(32-23)8-6-9-24(18)40-3)28(38)33-21(14-17-11-12-31-27(17)37)26(36)30-35-20-7-4-5-10-25(20)41-30/h4-10,15-17,21-22,26,32,36H,11-14H2,1-3H3,(H,31,37)(H,33,38)(H,34,39)/t17-,21-,22-,26-/m0/s1
InChIKeyDHQWCSDZTRDSRP-XIBGDNMGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](c2nc3ccccc3s2)O)NC(=O)c4cc5c([nH]4)cccc5OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)c4sc5ccccc5n4
ACDLabs 12.01C(C(NC(=O)C(NC(c2cc1c(OC)cccc1n2)=O)CC(C)C)CC3CCNC3=O)(c5nc4c(cccc4)s5)O
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1CCNC1=O)C(c2nc3ccccc3s2)O)NC(=O)c4cc5c([nH]4)cccc5OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)c4sc5ccccc5n4
FormulaC30 H35 N5 O5 S
NameN-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide;
GRL-024-20
ChEMBL
DrugBank
ZINC
PDB chain7jkv Chain B Residue 401 [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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PDB7jkv A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication.
Resolution1.25 Å
Binding residue
(original residue number in PDB)
T25 H41 M49 F140 N142 C145 H163 H164 M165 E166 Q189 T190 A191
Binding residue
(residue number reindexed from 1)
T26 H42 M50 F141 N143 C146 H164 H165 M166 E167 Q190 T191 A192
Annotation score1
Binding affinityBindingDB: EC50=4200nM,Ki=18nM
Enzymatic activity
Enzyme Commision number 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

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Biological Process
External links
PDB RCSB:7jkv, PDBe:7jkv, PDBj:7jkv
PDBsum7jkv
PubMed33510133
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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