Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T88015 | Target Info | |||
| Target Name | COVID-19 3C-like protease (3CLpro) | ||||
| Synonyms | COVID-19 3CL-PRO; COVID-19 3CLp; COVID-19 nsp5 | ||||
| Gene Name | COVID-19 rep | ||||
| Biochemical Class | Coronaviruses polyprotein 1ab family | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | acs.jmedchem.1c00409_ST.209 | Ligand Info | |||
| Canonical SMILES | CC(C)(C)OC(=O)NC1=CC=CN(C1=O)C(CC2CC2)C(=O)NC(CC3CCNC3=O)C(C(=O)NCC4=CC=CC=C4)O | ||||
| InChI | 1S/C31H41N5O7/c1-31(2,3)43-30(42)35-22-10-7-15-36(29(22)41)24(16-19-11-12-19)27(39)34-23(17-21-13-14-32-26(21)38)25(37)28(40)33-18-20-8-5-4-6-9-20/h4-10,15,19,21,23-25,37H,11-14,16-18H2,1-3H3,(H,32,38)(H,33,40)(H,34,39)(H,35,42)/t21-,23-,24-,25+/m0/s1 | ||||
| InChIKey | FRACPXUHUTXLCX-BELIEFIBSA-N | ||||
| PubChem Compound ID | 146018708 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6Y2F Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) | ||||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [1] |
| PDB Sequence |
SGFRKMAFPS
10 GKVEGCMVQV20 TCGTTTLNGL30 WLDDVVYCPR40 HVICTSMLNP52 NYEDLLIRKS 62 NHNFLVQAGN72 VQLRVIGHSM82 QNCVLKLKVD92 TANPKTPKYK102 FVRIQPGQTF 112 SVLACYNGSP122 SGVYQCAMRP132 NFTIKGSFLN142 GSCGSVGFNI152 DYDCVSFCYM 162 HHMELPTGVH172 AGTDLEGNFY182 GPFVDRQTAQ192 AAGTDTTITV202 NVLAWLYAAV 212 INGDRWFLNR222 FTTTLNDFNL232 VAMKYNYEPL242 TQDHVDILGP252 LSAQTGIAVL 262 DMCASLKELL272 QNGMNGRTIL282 GSALLEDEFT292 PFDVVRQCSG302 VTF |
|||||
|
|
THR26
3.380
LEU27
4.372
HIS41
2.681
MET49
3.625
TYR54
4.531
PHE140
3.198
LEU141
3.836
ASN142
3.329
GLY143
2.764
SER144
3.165
CYS145
1.807
|
|||||
| PDB ID: 6Y2G Crystal structure (orthorhombic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b) | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [1] |
| PDB Sequence |
SGFRKMAFPS
10 GKVEGCMVQV20 TCGTTTLNGL30 WLDDVVYCPR40 HVICTSEDML50 NPNYEDLLIR 60 KSNHNFLVQA70 GNVQLRVIGH80 SMQNCVLKLK90 VDTANPKTPK100 YKFVRIQPGQ 110 TFSVLACYNG120 SPSGVYQCAM130 RPNFTIKGSF140 LNGSCGSVGF150 NIDYDCVSFC 160 YMHHMELPTG170 VHAGTDLEGN180 FYGPFVDRQT190 AQAAGTDTTI200 TVNVLAWLYA 210 AVINGDRWFL220 NRFTTTLNDF230 NLVAMKYNYE240 PLTQDHVDIL250 GPLSAQTGIA 260 VLDMCASLKE270 LLQNGMNGRT280 ILGSALLEDE290 FTPFDVVRQC300 S |
|||||
|
|
THR25
4.971
THR26
3.528
LEU27
4.555
HIS41
2.812
MET49
3.534
TYR54
4.798
PHE140
3.096
LEU141
3.614
ASN142
3.479
GLY143
3.341
SER144
2.974
CYS145
1.812
|
|||||
| PDB ID: 8A4T crystal structures of diastereomer (S,S,S)-13b (13b-K) in complex with the SARS-CoV-2 Mpro | ||||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [2] |
| PDB Sequence |
SGFRKMAFPS
10 GKVEGCMVQV20 TCGTTTLNGL30 WLDDVVYCPR40 HVICTSEDML50 NPNYEDLLIR 60 KSNHNFLVQA70 GNVQLRVIGH80 SMQNCVLKLK90 VDTANPKTPK100 YKFVRIQPGQ 110 TFSVLACYNG120 SPSGVYQCAM130 RPNFTIKGSF140 LNGSCGSVGF150 NIDYDCVSFC 160 YMHHMELPTG170 VHAGTDLEGN180 FYGPFVDRQT190 AQAAGTDTTI200 TVNVLAWLYA 210 AVINGDRWFL220 NRFTTTLNDF230 NLVAMKYNYE240 PLTQDHVDIL250 GPLSAQTGIA 260 VLDMCASLKE270 LLQNGMNGRT280 ILGSALLEDE290 FTPFDVVRQC300 SGVTF |
|||||
|
|
THR26
4.113
LEU27
4.576
HIS41
2.574
MET49
3.219
TYR54
4.469
PHE140
3.265
LEU141
3.766
ASN142
2.938
GLY143
2.721
SER144
3.150
CYS145
1.789
|
|||||
| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved -ketoamide inhibitors. Science. 2020 Apr 24;368(6489):409-412. | ||||
| REF 2 | Diastereomeric Resolution Yields Highly Potent Inhibitor of SARS-CoV-2 Main Protease. J Med Chem. 2022 Oct 13;65(19):13328-13342. | ||||
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