Structure of PDB 7gkm Chain A Binding Site BS01

Receptor Information
>7gkm Chain A (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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG
Ligand information
Ligand IDQY6
InChIInChI=1S/C22H20ClN3O/c23-16-6-7-19-18(12-16)22(9-10-25-19)8-3-11-26(21(22)27)20-14-24-13-15-4-1-2-5-17(15)20/h1-2,4-7,12-14,25H,3,8-11H2/t22-/m1/s1
InChIKeyGMEVLWIDIJTOMX-JOCHJYFZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2N3CCC[C@@]4(C3=O)CCNc5c4cc(cc5)Cl
ACDLabs 12.01O=C1N(CCCC11CCNc2ccc(Cl)cc21)c1cncc2ccccc21
CACTVS 3.385Clc1ccc2NCC[C@]3(CCCN(C3=O)c4cncc5ccccc45)c2c1
CACTVS 3.385Clc1ccc2NCC[C]3(CCCN(C3=O)c4cncc5ccccc45)c2c1
OpenEye OEToolkits 2.0.7c1ccc2c(c1)cncc2N3CCCC4(C3=O)CCNc5c4cc(cc5)Cl
FormulaC22 H20 Cl N3 O
Name(3R)-6'-chloro-1-(isoquinolin-4-yl)-2',3'-dihydro-1'H-spiro[piperidine-3,4'-quinolin]-2-one
ChEMBL
DrugBank
ZINC
PDB chain7gkm Chain A Residue 407 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7gkm Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		M49 F140 L141 N142 C145 H163 H164 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		M49 F140 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

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Molecular Function
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Biological Process
External links
PDB RCSB:7gkm, PDBe:7gkm, PDBj:7gkm
PDBsum7gkm
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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