Structure of PDB 8j38 Chain A Binding Site BS01

Receptor Information
>8j38 Chain A (length=299) 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]
FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRHNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
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 chain8j38 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8j38 Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with PF00835231
Resolution1.72 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 C145 H163 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
H39 M47 F138 C143 H161 H162 M163 E164 Q187
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:8j38, PDBe:8j38, PDBj:8j38
PDBsum8j38
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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