Structure of PDB 7m00 Chain A Binding Site BS01

Receptor Information
>7m00 Chain A (length=295) 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]
FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGQLRVIGHSMQNCVLKLKVDTANPKTPKYKFV
RIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDY
DCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNV
LAWLYAAVINGDRWFLNFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSA
QTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Ligand information
Ligand IDYKA
InChIInChI=1S/C23H37F2N3O8S/c1-13(2)11-16(28-21(32)36-22(3,4)15-5-8-23(24,25)9-6-15)19(30)27-17(20(31)37(33,34)35)12-14-7-10-26-18(14)29/h10,13-17,20,31H,5-9,11-12H2,1-4H3,(H,27,30)(H,28,32)(H,33,34,35)/t14-,16-,17-,20+/m0/s1
InChIKeyAFVXFMYQWMALEA-JWWIWJDOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(C)C2CCC(CC2)(F)F
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)(C)C2CCC(CC2)(F)F
CACTVS 3.385CC(C)C[C@H](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CC=NC2=O)[C@H](O)[S](O)(=O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CC=NC2=O)[CH](O)[S](O)(=O)=O
ACDLabs 12.01O=C1N=CCC1CC(NC(=O)C(CC(C)C)NC(=O)OC(C)(C)C1CCC(F)(F)CC1)C(O)S(=O)(=O)O
FormulaC23 H37 F2 N3 O8 S
Name(1R,2S)-2-((S)-2-((((2-(4,4-difluorocyclohexyl)propan-2-yl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid
ChEMBL
DrugBank
ZINC
PDB chain7m00 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7m00 Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
Resolution2.0 Å
Binding residue
(original residue number in PDB)
H41 N142 C145 H163 H164 M165 E166 L167 P168 D187 Q189 T190 A191
Binding residue
(residue number reindexed from 1)
H39 N138 C141 H159 H160 M161 E162 L163 P164 D183 Q185 T186 A187
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:7m00, PDBe:7m00, PDBj:7m00
PDBsum7m00
PubMed34865476
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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