Structure of PDB 7gnk Chain B Binding Site BS01

Receptor Information
>7gnk Chain B (length=305) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF
Ligand information
Ligand IDS0X
InChIInChI=1S/C27H27ClN4O2/c28-21-8-7-20-15-31(16-25(33)30-12-18-5-6-18)17-27(23(20)11-21)9-10-32(26(27)34)24-14-29-13-19-3-1-2-4-22(19)24/h1-4,7-8,11,13-14,18H,5-6,9-10,12,15-17H2,(H,30,33)/t27-/m1/s1
InChIKeyRIGXBQKBYSFBJB-HHHXNRCGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2N3CCC4(C3=O)CN(Cc5c4cc(cc5)Cl)CC(=O)NCC6CC6
CACTVS 3.385Clc1ccc2CN(CC(=O)NCC3CC3)C[C@]4(CCN(C4=O)c5cncc6ccccc56)c2c1
CACTVS 3.385Clc1ccc2CN(CC(=O)NCC3CC3)C[C]4(CCN(C4=O)c5cncc6ccccc56)c2c1
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2N3CC[C@@]4(C3=O)CN(Cc5c4cc(cc5)Cl)CC(=O)NCC6CC6
ACDLabs 12.01Clc1ccc2CN(CC3(CCN(C3=O)c3cncc4ccccc43)c2c1)CC(=O)NCC1CC1
FormulaC27 H27 Cl N4 O2
Name2-[(3'S)-6-chloro-1'-(isoquinolin-4-yl)-2'-oxo-1H-spiro[isoquinoline-4,3'-pyrrolidin]-2(3H)-yl]-N-(cyclopropylmethyl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain7gnk Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7gnk Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.72 Å
Binding residue
(original residue number in PDB)		H41 M49 L141 N142 C145 H163 H164 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 L141 N142 C145 H163 H164 M165 E166 D187 R188 Q189
Annotation score1
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
View graph for
Biological Process
External links
PDB RCSB:7gnk, PDBe:7gnk, PDBj:7gnk
PDBsum7gnk
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]