Structure of PDB 8dcz Chain B Binding Site BS01

Receptor Information
>8dcz Chain B (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
NIDYDCVSFCYMHHYELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
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 chain8dcz Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dcz Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir.
Resolution2.38 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 L141 N142 C145 H163 H164 Y165 E166 R188 Q189 T190 A191
Binding residue
(residue number reindexed from 1)
H41 M49 F140 L141 N142 C145 H163 H164 Y165 E166 R188 Q189 T190 A191
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:8dcz, PDBe:8dcz, PDBj:8dcz
PDBsum8dcz
PubMed37637734
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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