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 Cysteine Sulfenic Acid Ligand Info
Canonical SMILES C(C(C(=O)O)N)SO
InChI 1S/C3H7NO3S/c4-2(1-8-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
InChIKey FXIRVRPOOYSARH-REOHCLBHSA-N
PubChem Compound ID 165339
Drug Binding Sites of Target  Top
PDB ID: 7JQ2      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI5
Method X-ray diffraction Resolution 1.40 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
FTPFDVVRQS
301

GVTFQ
Residue
Distance (Å)
PHE3
4.156
ALA210
3.781
ILE213
3.512
ASN214
3.830
ASP295
4.956
VAL296
3.017
Residue
Distance (Å)
VAL297
3.312
ARG298
3.262
GLN299
1.329
SER301
1.333
GLY302
3.823
PDB ID: 7JPZ      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI1
Method X-ray diffraction Resolution 1.60 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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Residue
Distance (Å)
PHE3
3.787
GLN110
4.286
THR111
3.207
PHE112
2.888
VAL114
3.425
TYR126
3.488
GLN127
1.324
ALA129
1.325
MET130
4.311
ILE136
3.466
LYS137
4.495
Residue
Distance (Å)
GLY138
4.294
ALA210
4.004
ILE213
3.644
ASN214
3.328
GLU290
3.350
VAL296
2.980
VAL297
3.400
ARG298
3.418
GLN299
1.336
SER301
1.333
GLY302
3.804
PDB ID: 7RVN      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI12
Method X-ray diffraction Resolution 1.63 Å Mutation No [2]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Residue
Distance (Å)
GLY2
4.935
PHE3
3.445
GLN110
4.280
THR111
3.116
PHE112
2.823
SER113
4.966
VAL114
3.630
TYR126
3.131
GLN127
1.322
ALA129
1.332
MET130
4.437
ILE136
3.987
LYS137
3.984
Residue
Distance (Å)
GLY138
4.038
ALA210
3.568
ILE213
4.251
ASN214
3.796
GLU290
3.602
ASP295
4.896
VAL296
2.896
VAL297
3.394
ARG298
3.351
GLN299
1.332
SER301
1.334
GLY302
3.906
PDB ID: 7JP0      Crystal structure of Mpro with inhibitor r1
Method X-ray diffraction Resolution 1.65 Å Mutation No [3]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:209 or .A:210 or .A:213 or .A:214 or .A:256 or .A:290 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.060
GLN110
4.197
THR111
3.094
PHE112
2.741
SER113
4.962
VAL114
3.623
TYR126
3.350
GLN127
1.326
ALA129
1.336
MET130
4.309
ILE136
3.917
LYS137
4.012
GLY138
4.279
Residue
Distance (Å)
TYR209
4.876
ALA210
3.613
ILE213
3.283
ASN214
3.973
GLN256
4.809
GLU290
3.556
VAL296
2.942
VAL297
3.286
ARG298
3.323
GLN299
1.329
SER301
1.334
GLY302
3.856
PDB ID: 7JQ0      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI3
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:209 or .A:210 or .A:213 or .A:214 or .A:256 or .A:290 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.102
GLN110
4.203
THR111
3.088
PHE112
2.734
SER113
4.966
VAL114
3.564
TYR126
3.364
GLN127
1.328
ALA129
1.335
MET130
4.286
ILE136
3.932
LYS137
4.059
GLY138
4.292
Residue
Distance (Å)
TYR209
4.826
ALA210
3.619
ILE213
3.211
ASN214
3.936
GLN256
4.807
GLU290
3.555
ASP295
4.989
VAL296
2.887
VAL297
3.287
ARG298
3.319
GLN299
1.329
SER301
1.335
GLY302
3.870
PDB ID: 7JQ1      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI4
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:209 or .A:210 or .A:213 or .A:214 or .A:256 or .A:290 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.187
GLN110
4.102
THR111
3.061
PHE112
2.916
VAL114
3.577
TYR126
3.066
GLN127
1.331
ALA129
1.324
MET130
4.332
ILE136
3.962
LYS137
4.039
GLY138
4.130
Residue
Distance (Å)
TYR209
4.993
ALA210
3.718
ILE213
3.328
ASN214
4.190
GLN256
4.832
GLU290
3.281
VAL296
2.979
VAL297
3.146
ARG298
3.286
GLN299
1.327
SER301
1.332
GLY302
3.934
PDB ID: 7JQ4      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI7
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:290 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.363
GLN110
4.206
THR111
3.089
PHE112
2.786
SER113
4.933
VAL114
3.559
TYR126
3.289
GLN127
1.328
ALA129
1.323
MET130
4.309
ILE136
4.020
LYS137
4.116
Residue
Distance (Å)
GLY138
4.197
ALA210
4.038
ILE213
3.577
ASN214
3.819
GLU290
3.502
VAL296
3.095
VAL297
3.468
ARG298
3.202
GLN299
1.341
SER301
1.332
GLY302
3.861
PDB ID: 7RVS      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI19
Method X-ray diffraction Resolution 1.85 Å Mutation No [2]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:290 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
3.518
GLN110
4.291
THR111
3.094
PHE112
2.809
SER113
4.978
VAL114
3.509
TYR126
3.012
GLN127
1.334
ALA129
1.333
MET130
4.401
ILE136
4.065
LYS137
4.084
Residue
Distance (Å)
GLY138
4.047
ALA210
3.341
ILE213
4.115
ASN214
3.981
GLU290
3.585
ASP295
4.871
VAL296
2.859
VAL297
3.304
ARG298
3.396
GLN299
1.333
SER301
1.338
GLY302
3.885
PDB ID: 7RVX      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI24
Method X-ray diffraction Resolution 1.85 Å Mutation No [2]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:209 or .A:210 or .A:213 or .A:214 or .A:290 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
3.644
GLN110
4.380
THR111
3.122
PHE112
2.870
SER113
4.956
VAL114
3.843
TYR126
3.013
GLN127
1.332
ALA129
1.336
MET130
4.498
ILE136
3.939
LYS137
3.710
GLY138
3.753
Residue
Distance (Å)
TYR209
4.770
ALA210
3.140
ILE213
3.781
ASN214
4.062
GLU290
3.656
ASP295
4.915
VAL296
2.806
VAL297
3.432
ARG298
3.454
GLN299
1.326
SER301
1.337
GLY302
3.812
PDB ID: 7JQ5      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI8
Method X-ray diffraction Resolution 1.90 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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:290 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.286
GLN110
4.235
THR111
3.103
PHE112
2.679
SER113
4.902
VAL114
3.556
TYR126
2.984
GLN127
1.328
ALA129
1.325
MET130
4.349
ILE136
3.821
LYS137
4.350
Residue
Distance (Å)
GLY138
4.189
ALA210
3.999
ILE213
3.307
ASN214
3.682
GLU290
3.574
VAL296
3.145
VAL297
3.553
ARG298
3.246
GLN299
1.333
SER301
1.331
GLY302
3.879
PDB ID: 7AWU      Structure of SARS-CoV-2 Main Protease bound to LSN2463359.
Method X-ray diffraction Resolution 2.07 Å Mutation No [4]
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
LNGSGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQCS
301

GVTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:27 or .A:28 or .A:39 or .A:41 or .A:140 or .A:141 or .A:142 or .A:143 or .A:144 or .A:146 or .A:147 or .A:163 or .A:164 or .A:165; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU27
2.362
ASN28
2.164
PRO39
3.155
HIS41
3.133
PHE140
4.969
LEU141
4.792
ASN142
4.070
Residue
Distance (Å)
GLY143
2.828
SER144
1.331
GLY146
1.327
SER147
2.777
HIS163
3.289
HIS164
3.213
MET165
4.894
PDB ID: 7JQ3      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI6
Method X-ray diffraction Resolution 2.10 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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:290 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
4.230
GLN110
4.214
THR111
3.051
PHE112
2.712
SER113
4.928
VAL114
3.531
TYR126
2.898
GLN127
1.329
ALA129
1.324
MET130
4.369
ILE136
4.087
LYS137
4.393
Residue
Distance (Å)
GLY138
4.279
ALA210
4.046
ILE213
3.361
ASN214
4.091
GLU290
3.620
VAL296
3.045
VAL297
3.411
ARG298
3.417
GLN299
1.327
SER301
1.331
GLY302
3.753
PDB ID: 7S6W      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI29
Method X-ray diffraction Resolution 2.29 Å Mutation No [5]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:290 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
3.106
GLN110
4.333
THR111
3.090
PHE112
2.842
SER113
4.994
VAL114
3.954
TYR126
3.096
GLN127
1.325
ALA129
1.326
MET130
4.370
ILE136
4.080
LYS137
3.667
Residue
Distance (Å)
GLY138
3.809
ALA210
3.753
ILE213
3.602
ASN214
3.875
GLU290
3.451
ASP295
4.859
VAL296
2.929
VAL297
3.389
ARG298
3.348
GLN299
1.329
SER301
1.329
GLY302
3.632
PDB ID: 7RVQ      Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI16
Method X-ray diffraction Resolution 2.48 Å Mutation No [2]
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
SPSGVYQAMR
131
PNFTIKGSFL
141
NGSCGSVGFN
151

IDYDCVSFCY
161
MHHMELPTGV
171
HAGTDLEGNF
181
YGPFVDRQTA
191
QAAGTDTTIT
201

VNVLAWLYAA
211
VINGDRWFLN
221
RFTTTLNDFN
231
LVAMKYNYEP
241
LTQDHVDILG
251

PLSAQTGIAV
261
LDMCASLKEL
271
LQNGMNGRTI
281
LGSALLEDEF
291
TPFDVVRQSG
302

VTFQ
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CSO or .CSO2 or .CSO3 or :3CSO;style chemicals stick;color identity;select .A:3 or .A:110 or .A:111 or .A:112 or .A:113 or .A:114 or .A:126 or .A:127 or .A:129 or .A:130 or .A:136 or .A:137 or .A:138 or .A:210 or .A:213 or .A:214 or .A:256 or .A:290 or .A:295 or .A:296 or .A:297 or .A:298 or .A:299 or .A:301 or .A:302; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE3
3.068
GLN110
4.894
THR111
3.430
PHE112
2.979
SER113
4.984
VAL114
3.494
TYR126
3.081
GLN127
1.329
ALA129
1.325
MET130
4.632
ILE136
4.163
LYS137
4.229
GLY138
4.102
Residue
Distance (Å)
ALA210
3.393
ILE213
4.096
ASN214
3.930
GLN256
4.729
GLU290
3.928
ASP295
4.982
VAL296
2.913
VAL297
3.267
ARG298
3.301
GLN299
1.331
SER301
1.330
GLY302
3.793
References  Top
REF 1 A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors*. ChemMedChem. 2021 Mar 18;16(6):942-948.
REF 2 A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals. Eur J Med Chem. 2022 Oct 5;240:114570.
REF 3 Crystal structure of Mpro with inhibitor r1
REF 4 X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science. 2021 May 7;372(6542):642-646.
REF 5 A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals. Eur J Med Chem. 2022 Oct 5;240:114596.

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