Structure of PDB 8r12 Chain B Binding Site BS01

Receptor Information
>8r12 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG
Ligand information
Ligand IDXH9
InChIInChI=1S/C19H19ClN4O/c20-18-10-17(12-22-13-18)19(25)24-7-3-6-23(8-9-24)14-16-5-2-1-4-15(16)11-21/h1-2,4-5,10,12-13H,3,6-9,14H2
InChIKeyVIHXPVLCTFBBEL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(c(c1)CN2CCCN(CC2)C(=O)c3cc(cnc3)Cl)C#N
CACTVS 3.385Clc1cncc(c1)C(=O)N2CCCN(CC2)Cc3ccccc3C#N
FormulaC19 H19 Cl N4 O
Name2-[[4-(5-chloranylpyridin-3-yl)carbonyl-1,4-diazepan-1-yl]methyl]benzenecarbonitrile
ChEMBL
DrugBank
ZINC
PDB chain8r12 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8r12 Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches
Resolution1.587 Å
Binding residue
(original residue number in PDB)		H41 F140 L141 N142 S144 C145 H163 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 F140 L141 N142 S144 C145 H163 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:8r12, PDBe:8r12, PDBj:8r12
PDBsum8r12
PubMed38911172
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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