Structure of PDB 7n3k Chain D Binding Site BS02

Receptor Information
>7n3k Chain D (length=124) 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]
AALEVLFQGPGNNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGR
FVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLY
FIKGLNNLNRGMVLGSLAATVRLQ
Ligand information
Ligand IDODN
InChIInChI=1S/C20H30O6/c1-9-10-4-5-11-18-8-26-20(25,19(11,14(9)22)15(10)23)16(24)13(18)17(2,3)7-6-12(18)21/h9-13,15-16,21,23-25H,4-8H2,1-3H3/t9-,10+,11+,12+,13-,15-,16+,18-,19+,20-/m1/s1
InChIKeyRWELMBQGCLVKOE-ZJOCIWLNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C[C@@H]1[C@@H]2CC[C@H]3[C@@]45CO[C@@]([C@]3([C@@H]2O)C1=O)([C@H]([C@@H]4C(CC[C@@H]5O)(C)C)O)O
CACTVS 3.385C[CH]1[CH]2CC[CH]3[C]45CO[C](O)([CH](O)[CH]4C(C)(C)CC[CH]5O)[C]3([CH]2O)C1=O
ACDLabs 12.01O=C2C(C)C4CCC3C51C(C(O)C(O)(OC1)C23C4O)C(CCC5O)(C)C
CACTVS 3.385C[C@@H]1[C@@H]2CC[C@H]3[C@@]45CO[C@](O)([C@@H](O)[C@@H]4C(C)(C)CC[C@@H]5O)[C@]3([C@@H]2O)C1=O
OpenEye OEToolkits 1.9.2CC1C2CCC3C45COC(C3(C2O)C1=O)(C(C4C(CCC5O)(C)C)O)O
FormulaC20 H30 O6
Name(1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one
ChEMBL
DrugBank
ZINCZINC000263621003
PDB chain7n3k Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7n3k A natural product compound inhibits coronaviral replication in vitro by binding to the conserved Nsp9 SARS-CoV-2 protein.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		P71 P72 C73
Binding residue
(residue number reindexed from 1)		P82 P83 C84
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
Biological Process
GO:0019079 viral genome replication

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Molecular Function
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Biological Process
External links
PDB RCSB:7n3k, PDBe:7n3k, PDBj:7n3k
PDBsum7n3k
PubMed34756886
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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