Structure of PDB 7gd2 Chain A Binding Site BS01

Receptor Information
>7gd2 Chain A (length=304) 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
SGVT
Ligand information
Ligand IDM26
InChIInChI=1S/C19H18BrFN2O3/c1-26-10-17(11-3-2-4-12(20)7-11)22-18(24)9-15-14-8-13(21)5-6-16(14)23-19(15)25/h2-8,15,17H,9-10H2,1H3,(H,22,24)(H,23,25)/t15-,17-/m0/s1
InChIKeyHRBNXNLHEPAYDR-RDJZCZTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC[CH](NC(=O)C[CH]1C(=O)Nc2ccc(F)cc12)c3cccc(Br)c3
ACDLabs 12.01Brc1cccc(c1)C(COC)NC(=O)CC1c2cc(F)ccc2NC1=O
OpenEye OEToolkits 2.0.7COCC(c1cccc(c1)Br)NC(=O)CC2c3cc(ccc3NC2=O)F
CACTVS 3.385COC[C@H](NC(=O)C[C@@H]1C(=O)Nc2ccc(F)cc12)c3cccc(Br)c3
OpenEye OEToolkits 2.0.7COC[C@@H](c1cccc(c1)Br)NC(=O)C[C@H]2c3cc(ccc3NC2=O)F
FormulaC19 H18 Br F N2 O3
NameN-[(1R)-1-(3-bromophenyl)-2-methoxyethyl]-2-[(3S)-5-fluoro-2-oxo-2,3-dihydro-1H-indol-3-yl]acetamide
ChEMBL
DrugBank
ZINC
PDB chain7gd2 Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7gd2 Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.65 Å
Binding residue
(original residue number in PDB)		H41 M49 F140 L141 N142 H163 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 F140 L141 N142 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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7gd2, PDBe:7gd2, PDBj:7gd2
PDBsum7gd2
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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