Structure of PDB 8r0v Chain C Binding Site BS01

Receptor Information
>8r0v Chain C (length=305) 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
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRHNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF
Ligand information
Ligand IDO6K
InChIInChI=1S/C31H41N5O7/c1-31(2,3)43-30(42)35-22-10-7-15-36(29(22)41)24(16-19-11-12-19)27(39)34-23(17-21-13-14-32-26(21)38)25(37)28(40)33-18-20-8-5-4-6-9-20/h4-10,15,19,21,23-25,37H,11-14,16-18H2,1-3H3,(H,32,38)(H,33,40)(H,34,39)(H,35,42)/t21-,23-,24-,25+/m0/s1
InChIKeyFRACPXUHUTXLCX-BELIEFIBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(C)OC(=O)NC1=CC=CN(C1=O)C(CC2CC2)C(=O)NC(CC3CCNC3=O)C(C(=O)NCc4ccccc4)O
OpenEye OEToolkits 2.0.7CC(C)(C)OC(=O)NC1=CC=CN(C1=O)[C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](C(=O)NCc4ccccc4)O
CACTVS 3.385CC(C)(C)OC(=O)NC1=CC=CN([CH](CC2CC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(=O)NCc4ccccc4)C1=O
CACTVS 3.385CC(C)(C)OC(=O)NC1=CC=CN([C@@H](CC2CC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)C(=O)NCc4ccccc4)C1=O
FormulaC31 H41 N5 O7
Name~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate;
(S,S,S)-13b;
13b-K;
ketoamide inhibitor 13b (bound)
ChEMBL
DrugBank
ZINC
PDB chain8r0v Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8r0v SARS-CoV-2 Omicron (P132H) complex with alpha-ketoamide 13b-K at pH 6.5
Resolution2.48 Å
Binding residue
(original residue number in PDB)
T26 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 L167 D187 R188 Q189
Binding residue
(residue number reindexed from 1)
T26 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 L167 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:8r0v, PDBe:8r0v, PDBj:8r0v
PDBsum8r0v
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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