Structure of PDB 7l13 Chain A Binding Site BS01

Receptor Information
>7l13 Chain A (length=301) 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
S
Ligand information
Ligand IDXF7
InChIInChI=1S/C27H18Cl2N4O4/c28-19-8-17(9-21(11-19)37-15-16-4-1-2-6-24(16)29)22-10-18(23-13-31-27(36)32-25(23)34)14-33(26(22)35)20-5-3-7-30-12-20/h1-14H,15H2,(H2,31,32,34,36)
InChIKeyNFXZAFCZOMISJH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(c(c1)COc2cc(cc(c2)Cl)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O)Cl
ACDLabs 12.01C2(N(c1cnccc1)C=C(C=C2c3cc(cc(c3)OCc4ccccc4Cl)Cl)C=5C(=O)NC(=O)NC=5)=O
CACTVS 3.385Clc1cc(OCc2ccccc2Cl)cc(c1)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O
FormulaC27 H18 Cl2 N4 O4
Name(5S)-5-(3-{3-chloro-5-[(2-chlorophenyl)methoxy]phenyl}-2-oxo[2H-[1,3'-bipyridine]]-5-yl)pyrimidine-2,4(3H,5H)-dione
ChEMBLCHEMBL5180524
DrugBank
ZINC
PDB chain7l13 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7l13 Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.
Resolution2.17 Å
Binding residue
(original residue number in PDB)		T25 T26 H41 M49 F140 L141 N142 G143 C145 H163 M165 E166 P168 D187 Q189
Binding residue
(residue number reindexed from 1)		T25 T26 H41 M49 F140 L141 N142 G143 C145 H163 M165 E166 P168 D187 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:7l13, PDBe:7l13, PDBj:7l13
PDBsum7l13
PubMed33786375
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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