Structure of PDB 7s72 Chain A Binding Site BS01

Receptor Information
>7s72 Chain A (length=300) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICNPNYED
LLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI
QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDC
VSFCYMHHMELPTGVHAGTDLAGNFYGPFVDRQTAQAAGTDTTITVNVLA
WLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQ
TGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ
Ligand information
Ligand ID8I0
InChIInChI=1S/C34H52N6O6/c1-32(2,3)26(38-31(46)39-33(4,5)6)30(45)40-18-21-23(34(21,7)8)24(40)28(43)37-22(16-20-14-15-35-27(20)42)25(41)29(44)36-17-19-12-10-9-11-13-19/h9-13,20-26,41H,14-18H2,1-8H3,(H,35,42)(H,36,44)(H,37,43)(H2,38,39,46)/t20-,21-,22-,23-,24-,25+,26+/m0/s1
InChIKeyWFDSDFTYLISRSE-ADSPCUKESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)NC(=O)N[CH](C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(=O)NCc4ccccc4)C2(C)C)C(C)(C)C
OpenEye OEToolkits 2.0.7CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)NC(C)(C)C)C(=O)NC(CC3CCNC3=O)C(C(=O)NCc4ccccc4)O)C
CACTVS 3.385CC(C)(C)NC(=O)N[C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)C(=O)NCc4ccccc4)C2(C)C)C(C)(C)C
OpenEye OEToolkits 2.0.7CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)NC(C)(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](C(=O)NCc4ccccc4)O)C
ACDLabs 12.01CC1(C)C2C(C(=O)NC(CC3CCNC3=O)C(O)C(=O)NCc3ccccc3)N(CC21)C(=O)C(NC(=O)NC(C)(C)C)C(C)(C)C
FormulaC34 H52 N6 O6
Name(1R,2S,5S)-N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7s72 Chain A Residue 401 [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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PDB7s72 A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		T24 T25 T26 H41 N142 G143 S144 C145 H163 H164 M165 E166 Q189 T190 Q192
Binding residue
(residue number reindexed from 1)		T24 T25 T26 H41 N136 G137 S138 C139 H157 H158 M159 E160 Q183 T184 Q186
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7s72, PDBe:7s72, PDBj:7s72
PDBsum7s72
PubMed35839690
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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