Structure of PDB 6y2g Chain A Binding Site BS01

Receptor Information
>6y2g 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 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 chain6y2g Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6y2g Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 N142 G143 S144 C145 H163 H164 M165 E166 D187 Q189
Binding residue
(residue number reindexed from 1)
H41 M49 F140 N142 G143 S144 C145 H163 H164 M165 E166 D187 Q189
Annotation score1
Binding affinityBindingDB: IC50=670nM,Ki=900nM
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:6y2g, PDBe:6y2g, PDBj:6y2g
PDBsum6y2g
PubMed32198291
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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