Structure of PDB 9auj Chain A Binding Site BS01

Receptor Information
>9auj 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
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGACGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF
Ligand information
Ligand ID4WI
InChIInChI=1S/C23H34F3N5O4/c1-21(2,3)16(30-20(35)23(24,25)26)19(34)31-10-13-14(22(13,4)5)15(31)18(33)29-12(9-27)8-11-6-7-28-17(11)32/h9,11-16,27H,6-8,10H2,1-5H3,(H,28,32)(H,29,33)(H,30,35)/b27-9+/t11-,12-,13-,14-,15-,16+/m0/s1
InChIKeyWDVIRQQKRMIXGS-XIFHJVQQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C=N)C2(C)C
OpenEye OEToolkits 2.0.7[H]/N=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F
ACDLabs 12.01CC1(C)C2C(C(=O)NC(C=N)CC3CCNC3=O)N(CC21)C(=O)C(NC(=O)C(F)(F)F)C(C)(C)C
OpenEye OEToolkits 2.0.7CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C=N)C
CACTVS 3.385CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)C=N)C2(C)C
FormulaC23 H34 F3 N5 O4
Name(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide;
PF-07321332, bound form;
nirmatrelvir, bound form;
Paxlovid, bound form
ChEMBL
DrugBank
ZINC
PDB chain9auj 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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PDB9auj In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance.
Resolution1.486 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 C145 H163 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
H41 M49 F140 C145 H163 H164 M165 E166 Q189
Annotation score1
External links
PDB RCSB:9auj, PDBe:9auj, PDBj:9auj
PDBsum9auj
PubMed39047088
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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