Structure of PDB 9bpf Chain A Binding Site BS01

Receptor Information
>9bpf Chain A (length=305) 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
SGVTF
Ligand information
Ligand IDYDL
InChIInChI=1S/C21H32F3N5O5/c1-20(2,3)15(28-19(33)34-4)18(32)29-10-12(21(22,23)24)8-14(29)17(31)27-13(9-25)7-11-5-6-26-16(11)30/h9,11-15,25H,5-8,10H2,1-4H3,(H,26,30)(H,27,31)(H,28,33)/t11-,12+,13-,14-,15+/m0/s1
InChIKeyDTVPKRIYQXLPLE-AIEDFZFUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)N[C@H](C(=O)N1C[C@@H](C[C@H]1C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=N)C(F)(F)F)C(C)(C)C
OpenEye OEToolkits 2.0.7CC(C)(C)[C@@H](C(=O)N1C[C@@H](C[C@H]1C(=O)N[C@@H](C[C@@H]2CCNC2=O)C=N)C(F)(F)F)NC(=O)OC
CACTVS 3.385COC(=O)N[CH](C(=O)N1C[CH](C[CH]1C(=O)N[CH](C[CH]2CCNC2=O)C=N)C(F)(F)F)C(C)(C)C
OpenEye OEToolkits 2.0.7CC(C)(C)C(C(=O)N1CC(CC1C(=O)NC(CC2CCNC2=O)C=N)C(F)(F)F)NC(=O)OC
ACDLabs 12.01FC(F)(F)C1CC(C(=O)NC(C=N)CC2CCNC2=O)N(C1)C(=O)C(NC(=O)OC)C(C)(C)C
FormulaC21 H32 F3 N5 O5
NameN-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-(trifluoromethyl)-L-prolinamide;
Ibuzatrelvir, bound form;
N-(methoxycarbonyl)-3-methyl-L-valyl-(4R)-N-{(1S)-1-cyano-2-[(3S)-2-oxopyrrolidin-3-yl]ethyl}-4-(trifluoromethyl)-L-prolinamide, bound form
ChEMBL
DrugBank
ZINC
PDB chain9bpf 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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PDB9bpf A Structural Comparison of Oral SARS-CoV-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (Mpro) of SARS-CoV-2 and MERS-CoV
Resolution2.0 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 C145 H163 H164 M165 E166 R188 Q189
Binding residue
(residue number reindexed from 1)
H41 M49 F140 C145 H163 H164 M165 E166 R188 Q189
Annotation score1
External links
PDB RCSB:9bpf, PDBe:9bpf, PDBj:9bpf
PDBsum9bpf
PubMed39211604
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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