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Structure of PDB 7tdu Chain A Binding Site BS01

Receptor Information
>7tdu Chain A (length=306) 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
SGVTFQ
Ligand information
Ligand IDI1W
InChIInChI=1S/C33H48N6O5S/c1-31(2,3)25(37-30(44)38-32(4,5)6)29(43)39-16-18-22(33(18,7)8)23(39)27(42)35-20(15-17-13-14-34-26(17)41)24(40)28-36-19-11-9-10-12-21(19)45-28/h9-12,17-18,20,22-25,40H,13-16H2,1-8H3,(H,34,41)(H,35,42)(H2,37,38,44)/t17-,18-,20-,22-,23-,24-,25+/m0/s1/i/hD4
InChIKeyARSJHDLARMCGPB-GBACRSPZSA-N
SMILES
SoftwareSMILES
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](c4nc5ccccc5s4)O)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(c4nc5ccccc5s4)O)C
CACTVS 3.385CC(C)(C)N(C(=O)N([CH](C(=O)N1C[CH]2[CH]([CH]1C(=O)N([CH](C[CH]3CCN(C3=O)[2H])[CH](O)c4sc5ccccc5n4)[2H])C2(C)C)C(C)(C)C)[2H])[2H]
ACDLabs 12.01CC(C)(C)N([2H])C(=O)N([2H])C(C(=O)N1CC2C(C1C(=O)N([2H])C(CC1CCN([2H])C1=O)C(O)c1nc3ccccc3s1)C2(C)C)C(C)(C)C
CACTVS 3.385CC(C)(C)N(C(=O)N([C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N([C@@H](C[C@@H]3CCN(C3=O)[2H])[C@H](O)c4sc5ccccc5n4)[2H])C2(C)C)C(C)(C)C)[2H])[2H]
FormulaC33 H48 N6 O5 S
Name(1R,2S,5S)-N-{(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxo(1-~2~H)pyrrolidin-3-yl]propan-2-yl}-3-{N-[tert-butyl(~2~H)carbamoyl]-3-methyl-L-(N-~2~H)valyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-(~2~H)carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7tdu 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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PDB7tdu Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease
Resolution1.85 Å
Binding residue
(original residue number in PDB)
T25 L27 H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 H172 Q189 Q192
Binding residue
(residue number reindexed from 1)
T25 L27 H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 H172 Q189 Q192
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.-
External links
PDB RCSB:7tdu, PDBe:7tdu, PDBj:7tdu
PDBsum7tdu
PubMed35477935
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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