Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
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
R1AB_SARS2 (3264 - 3569)
Ligand General Information  Top
Ligand Name (1R,2S)-2-((S)-2-(((((1R,3s,5S)-bicyclo[3.3.1]nonan-3-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid Ligand Info
Drug Binding Sites of Target  Top
PDB ID: 7LKR      1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 2a
Method X-ray diffraction Resolution 1.65 Å Mutation No [1]
PDB Sequence
KMAFPSGKVE
14
GCMVQVTCGT
24
TTLNGLWLDD
34
VVYCPRHVIC
44
TSEDMLNPNY
54

EDLLIRKSNH
64
NFLVQAGNVQ
74
LRVIGHSMQN
84
CVLKLKVDTA
94
NPKTPKYKFV
104

RIQPGQTFSV
114
LACYNGSPSG
124
VYQCAMRPNF
134
TIKGSFLNGS
144
CGSVGFNIDY
154

DCVSFCYMHH
164
MELPTGVHAG
174
TDLEGNFYGP
184
FVDRQTAQAA
194
GTDTTITVNV
204

LAWLYAAVIN
214
GDRWFLNRFT
224
TTLNDFNLVA
234
MKYNYEPLTQ
244
DHVDILGPLS
254

AQTGIAVLDM
264
CASLKELLQN
274
GMNGRTILGS
284
ALLEDEFTPF
294
DVVRQC
Residue
Distance (Å)
LEU27
4.378
HIS41
2.981
MET49
3.976
TYR54
4.477
PHE140
3.307
LEU141
3.853
ASN142
3.749
GLY143
4.466
SER144
3.916
CYS145
1.799
Residue
Distance (Å)
HIS163
2.752
HIS164
3.023
MET165
3.510
GLU166
2.958
HIS172
3.464
VAL186
4.891
ASP187
3.831
ARG188
4.024
GLN189
2.938
PDB ID: 7LKU      1.65 A resolution structure of SARS-CoV-2 3CL protease in complex with inhibitor 3b (deuterated analog of inhibitor 2a)
Method X-ray diffraction Resolution 1.65 Å Mutation No [1]
PDB Sequence
SGFRKMAFPS
10
GKVEGCMVQV
20
TCGTTTLNGL
30
WLDDVVYCPR
40
HVICTSEDML
50

NPNYEDLLIR
60
KSNHNFLVQA
70
GNVQLRVIGH
80
SMQNCVLKLK
90
VDTANPKTPK
100

YKFVRIQPGQ
110
TFSVLACYNG
120
SPSGVYQCAM
130
RPNFTIKGSF
140
LNGSCGSVGF
150

NIDYDCVSFC
160
YMHHMELPTG
170
VHAGTDLEGN
180
FYGPFVDRQT
190
AQAAGTDTTI
200

TVNVLAWLYA
210
AVINGDRWFL
220
NRFTTTLNDF
230
NLVAMKYNYE
240
PLTQDHVDIL
250

GPLSAQTGIA
260
VLDMCASLKE
270
LLQNGMNGRT
280
ILGSALLEDE
290
FTPFDVVRQC
300
Residue
Distance (Å)
LEU27
4.315
HIS41
2.900
MET49
4.850
TYR54
4.588
PHE140
3.405
LEU141
3.846
ASN142
3.815
GLY143
4.532
SER144
3.927
CYS145
1.803
Residue
Distance (Å)
HIS163
2.779
HIS164
2.968
MET165
3.529
GLU166
2.951
HIS172
3.463
VAL186
4.764
ASP187
3.820
ARG188
4.008
GLN189
2.990
References  Top
REF 1 Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease. J Med Chem. 2021 Jul 22;64(14):10047-10058.

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