Structure of PDB 8j3a Chain B Binding Site BS01

Receptor Information
>8j3a Chain B (length=290) 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]
FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICCEDLLIRK
SNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQT
FSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCY
MHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAA
VINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAV
LDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
Ligand information
Ligand IDV2M
InChIInChI=1S/C24H34N4O6/c1-13(2)9-18(23(32)27-17(20(30)12-29)10-14-7-8-25-22(14)31)28-24(33)19-11-15-16(26-19)5-4-6-21(15)34-3/h4-6,11,13-14,17-18,20,26,29-30H,7-10,12H2,1-3H3,(H,25,31)(H,27,32)(H,28,33)/t14-,17-,18-,20+/m0/s1
InChIKeyFDQSUXUTXIGUIA-PRIDNEQBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C(O)CO
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1CCNC1=O)C(CO)O)NC(=O)c2cc3c([nH]2)cccc3OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)CO
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](CO)O)NC(=O)c2cc3c([nH]2)cccc3OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)CO
FormulaC24 H34 N4 O6
NameN-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide;
N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form
ChEMBL
DrugBank
ZINC
PDB chain8j3a Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8j3a Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with PF00835231
Resolution1.91 Å
Binding residue
(original residue number in PDB)
H41 F140 L141 N142 C145 H163 H164 M165 E166 Q189 T190 A191
Binding residue
(residue number reindexed from 1)
H39 F129 L130 N131 C134 H152 H153 M154 E155 Q178 T179 A180
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.50: mRNA guanylyltransferase.
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:8j3a, PDBe:8j3a, PDBj:8j3a
PDBsum8j3a
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]