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 Deuterium Oxide Ligand Info
Canonical SMILES O
InChI 1S/H2O/h1H2/i/hD2
InChIKey XLYOFNOQVPJJNP-ZSJDYOACSA-N
PubChem Compound ID 24602
Drug Binding Sites of Target  Top
PDB ID: 7TDU      Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with BBH-1
Method X-ray diffraction Resolution 1.85 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

SGVTFQ
Residue
Distance (Å)
SER1
1.872
GLY2
2.023
PHE3
3.369
ARG4
2.042
LYS5
1.747
MET6
1.911
ALA7
2.355
PHE8
2.169
PRO9
2.707
SER10
3.824
GLY11
2.902
LYS12
1.807
VAL13
3.394
GLU14
3.114
GLY15
3.002
CYS16
2.951
MET17
2.421
VAL18
2.809
GLN19
2.247
VAL20
3.596
THR21
2.320
THR25
4.060
THR26
2.843
LEU27
2.031
ASN28
2.929
LEU30
4.713
LEU32
2.247
ASP33
1.869
ASP34
2.203
VAL35
2.570
TYR37
1.906
ARG40
2.534
ILE43
1.633
CYS44
3.082
THR45
2.653
GLU47
2.396
ASP48
2.334
MET49
2.758
LEU50
2.676
ASN51
2.168
PRO52
1.842
ASN53
2.288
TYR54
2.347
GLU55
2.166
ASP56
3.128
LEU57
2.103
LEU58
3.111
ILE59
2.530
ARG60
2.145
LYS61
2.110
SER62
2.257
ASN63
3.083
HIS64
2.522
PHE66
2.040
LEU67
2.290
VAL68
1.999
GLN69
2.337
ALA70
3.057
GLY71
2.774
GLN74
2.253
LEU75
1.692
ARG76
3.022
VAL77
2.143
ILE78
3.292
GLY79
2.773
HIS80
2.108
SER81
1.995
MET82
2.004
GLN83
1.821
ASN84
1.771
CYS85
2.699
VAL86
3.123
LYS88
2.092
LEU89
3.573
LYS90
3.015
VAL91
2.727
ASP92
3.224
THR93
4.504
LYS97
1.898
THR98
3.083
PRO99
2.688
LYS100
2.275
TYR101
2.195
LYS102
2.169
PHE103
1.941
VAL104
2.076
ARG105
2.093
ILE106
1.863
GLN107
2.079
PRO108
2.006
GLY109
2.762
GLN110
2.260
THR111
2.090
PHE112
2.902
SER113
4.030
VAL114
4.413
LEU115
1.629
ALA116
3.022
CYS117
3.400
TYR118
1.777
ASN119
1.688
GLY120
1.922
SER121
3.637
PRO122
4.135
SER123
4.258
VAL125
4.519
TYR126
2.781
GLN127
1.722
CYS128
2.470
ALA129
1.776
MET130
3.972
ARG131
2.681
PRO132
1.856
ASN133
1.800
PHE134
1.818
THR135
2.253
ILE136
2.832
LYS137
2.000
GLY138
2.076
SER139
2.065
PHE140
2.883
LEU141
2.186
ASN142
2.168
GLY143
1.687
Residue
Distance (Å)
SER144
3.771
CYS145
2.854
GLY146
4.476
SER147
2.386
VAL148
1.935
PHE150
3.639
ASN151
1.725
ILE152
3.035
ASP153
2.304
TYR154
2.836
ASP155
2.574
CYS156
2.895
VAL157
4.441
SER158
2.215
PHE159
2.966
CYS160
2.276
TYR161
3.706
GLU166
1.783
LEU167
2.727
PRO168
2.378
THR169
4.883
GLY170
1.834
VAL171
2.350
HIS172
2.397
ALA173
2.417
GLY174
2.114
THR175
4.478
ASP176
1.926
LEU177
1.849
GLU178
1.778
GLY179
3.809
ASN180
1.912
PHE181
1.909
TYR182
1.862
GLY183
1.824
PRO184
2.346
PHE185
2.001
VAL186
2.336
ASP187
2.150
ARG188
2.342
GLN189
2.359
THR190
3.147
ALA191
4.153
GLN192
3.195
ALA193
4.443
ALA194
2.903
GLY195
1.681
THR196
2.318
ASP197
1.872
THR198
2.992
THR199
2.926
ILE200
2.819
THR201
2.797
VAL202
2.031
ASN203
1.920
VAL204
2.904
ALA206
3.609
TRP207
2.130
ALA211
4.743
VAL212
1.776
ILE213
2.540
ASN214
2.951
GLY215
2.966
ASP216
2.498
ARG217
1.991
TRP218
3.088
PHE219
1.614
LEU220
3.028
ASN221
1.998
ARG222
4.802
PHE223
4.257
ALA234
4.381
MET235
2.639
TYR237
4.905
ASN238
2.314
TYR239
1.859
GLU240
2.258
PRO241
1.946
LEU242
3.505
THR243
2.041
ASP245
3.122
HIS246
2.584
GLN256
3.292
THR257
2.977
GLY258
3.247
ILE259
2.526
ALA260
2.028
ASP263
1.865
MET264
3.232
ALA266
3.781
SER267
1.765
LEU268
3.674
GLU270
2.295
LEU271
2.610
LEU272
4.143
MET276
4.698
ARG279
2.387
THR280
2.696
ILE281
3.589
LEU282
2.356
GLY283
2.187
SER284
2.704
ALA285
2.113
LEU286
2.720
LEU287
1.942
GLU288
1.630
ASP289
2.043
GLU290
1.580
PHE291
2.074
THR292
1.748
PRO293
2.969
PHE294
2.600
ASP295
1.710
VAL296
3.679
ARG298
1.735
GLN299
1.679
CYS300
2.793
SER301
4.141
GLY302
2.634
VAL303
2.499
THR304
2.162
PHE305
2.862
GLN306
3.502
PDB ID: 7LB7      Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with Telaprevir
Method X-ray diffraction Resolution 2.00 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
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

SGVTFQ
Residue
Distance (Å)
SER1
1.926
GLY2
2.173
PHE3
2.035
ARG4
1.655
LYS5
2.109
MET6
1.768
ALA7
2.414
PHE8
1.960
GLY11
4.297
VAL13
3.413
GLU14
2.392
MET17
2.435
GLN19
2.029
VAL20
2.650
THR21
1.896
CYS22
2.762
GLY23
2.364
THR24
1.593
THR25
2.042
THR26
2.167
LEU27
2.194
ASN28
3.222
PRO39
3.396
ARG40
2.388
HIS41
1.702
VAL42
2.432
ILE43
2.118
CYS44
1.838
THR45
2.619
SER46
2.154
GLU47
4.267
ASP48
3.100
MET49
2.529
LEU50
3.113
ASN51
3.594
PRO52
2.209
ASN53
1.868
TYR54
2.155
GLU55
2.112
ASP56
4.733
LEU57
2.640
ARG60
4.357
LYS61
2.455
SER62
2.526
ASN63
2.044
HIS64
4.620
ASN65
4.331
PHE66
2.400
LEU67
1.872
VAL68
1.800
GLN69
2.569
GLN74
3.849
LEU75
1.759
ARG76
3.000
VAL77
2.649
GLY79
4.935
HIS80
2.773
MET82
3.222
GLN83
2.863
ASN84
1.817
CYS85
2.965
VAL86
4.819
LYS97
4.491
TYR101
2.312
LYS102
2.404
PHE103
2.099
VAL104
1.970
ARG105
2.264
ILE106
3.505
PRO108
2.684
GLY109
3.129
GLN110
2.327
THR111
1.989
PHE112
2.786
SER113
3.300
VAL114
4.997
LEU115
1.508
ALA116
2.870
CYS117
2.250
TYR118
1.759
ASN119
1.986
GLY120
3.714
PRO122
4.993
SER123
1.855
GLY124
2.632
VAL125
2.464
TYR126
2.384
GLN127
1.960
CYS128
2.940
ALA129
1.804
MET130
4.036
ARG131
2.570
PRO132
2.062
ASN133
1.905
PHE134
1.841
THR135
2.357
ILE136
2.734
LYS137
1.880
GLY138
3.244
SER139
2.628
PHE140
2.684
LEU141
2.009
ASN142
2.080
GLY143
1.774
SER144
2.987
CYS145
4.738
GLY146
4.682
SER147
2.731
VAL148
2.075
PHE150
3.489
ASN151
1.730
SER158
2.617
PHE159
2.687
CYS160
2.352
TYR161
3.743
HIS163
1.917
Residue
Distance (Å)
HIS164
2.124
MET165
4.250
GLU166
2.116
LEU167
2.269
PRO168
2.187
THR169
1.999
GLY170
1.890
VAL171
2.124
HIS172
3.001
ALA173
2.642
GLY174
2.200
THR175
4.772
ASP176
2.105
LEU177
1.898
GLU178
1.783
GLY179
4.128
ASN180
2.197
PHE181
1.954
TYR182
1.816
GLY183
1.808
PRO184
1.780
PHE185
1.999
VAL186
2.275
ASP187
1.925
ARG188
2.652
GLN189
1.853
THR190
2.926
ALA191
1.885
GLN192
1.743
ALA193
2.503
ALA194
1.738
GLY195
1.805
THR196
2.330
ASP197
3.287
THR198
2.400
THR199
4.001
ILE200
3.028
THR201
2.595
VAL202
1.971
ASN203
1.801
VAL204
2.914
LEU205
4.958
ALA206
3.572
TRP207
1.921
TYR209
4.986
ILE213
3.163
ASN214
3.844
GLY215
3.415
ASP216
2.791
ARG217
2.244
TRP218
2.487
PHE219
1.944
LEU220
4.124
ASN221
3.352
THR224
2.516
THR225
2.744
THR226
1.805
LEU227
1.930
ASN228
2.180
ASP229
1.604
PHE230
3.801
LEU232
2.416
VAL233
2.154
MET235
2.391
LYS236
4.412
TYR237
3.494
ASN238
3.151
TYR239
1.594
GLU240
1.763
PRO241
2.233
LEU242
2.709
THR243
3.203
GLN244
4.492
HIS246
2.455
VAL247
1.862
ASP248
2.917
ILE249
2.691
LEU250
3.761
GLY251
2.921
SER254
3.215
GLN256
3.543
GLY258
3.253
ILE259
2.181
ALA260
1.897
VAL261
1.920
LEU262
2.240
ASP263
1.966
ALA266
4.389
SER267
1.736
LEU268
3.744
LYS269
3.645
GLU270
2.262
LEU271
2.153
LEU272
3.937
THR280
1.977
ILE281
3.383
LEU282
2.659
GLY283
1.828
SER284
2.925
ALA285
2.450
LEU286
2.470
LEU287
2.159
GLU288
1.768
ASP289
2.117
GLU290
2.124
PHE291
2.117
THR292
2.004
PRO293
2.428
PHE294
2.291
ASP295
1.820
VAL296
3.711
ARG298
1.887
GLN299
2.053
CYS300
1.653
SER301
3.793
PDB ID: 7N8C      Joint X-ray/neutron structure of SARS-CoV-2 main protease (Mpro) in complex with Mcule5948770040
Method X-ray diffraction Resolution 2.20 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
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

SGVTFQ
Residue
Distance (Å)
SER1
1.832
GLY2
1.753
PHE3
3.220
ARG4
2.358
LYS5
1.995
MET6
1.919
ALA7
2.433
PHE8
2.325
PRO9
2.201
SER10
3.567
GLY11
2.972
LYS12
1.759
VAL13
3.393
GLU14
1.968
GLY15
3.128
CYS16
3.962
MET17
2.905
GLN19
2.273
VAL20
3.342
THR21
1.848
THR25
2.520
THR26
3.137
LEU27
2.622
ASN28
2.945
LEU30
4.717
LEU32
2.988
ASP33
2.351
ASP34
2.597
VAL35
2.851
TYR37
1.923
PRO39
2.694
ARG40
2.602
HIS41
1.855
VAL42
2.663
CYS44
4.752
MET49
3.660
PRO52
3.651
ASN53
2.879
TYR54
2.387
GLU55
3.301
LEU58
3.487
ASN63
3.903
PHE66
2.613
LEU67
2.235
VAL68
1.889
GLN69
2.581
GLN74
2.746
LEU75
1.540
ARG76
3.066
VAL77
3.022
ILE78
2.996
GLY79
2.899
HIS80
2.197
SER81
1.723
MET82
2.077
GLN83
1.644
ASN84
2.039
CYS85
3.218
VAL86
3.267
LYS88
1.957
LEU89
3.427
LYS90
3.046
VAL91
2.022
ASP92
2.488
THR93
4.090
LYS97
2.771
THR98
2.924
PRO99
2.416
LYS100
2.208
TYR101
2.020
LYS102
2.872
PHE103
1.936
VAL104
2.243
ARG105
1.900
ILE106
1.890
GLN107
2.003
PRO108
1.740
GLY109
2.616
GLN110
2.150
THR111
2.128
PHE112
3.149
SER113
3.580
VAL114
4.841
LEU115
1.747
ALA116
3.148
CYS117
3.049
TYR118
1.713
ASN119
1.810
GLY120
3.977
PRO122
4.410
SER123
2.589
GLY124
2.966
VAL125
4.467
TYR126
2.788
GLN127
1.969
CYS128
2.931
ALA129
1.812
MET130
3.917
ARG131
2.473
PRO132
2.029
ASN133
1.754
PHE134
1.863
THR135
2.160
ILE136
2.453
LYS137
1.909
GLY138
2.350
SER139
1.679
PHE140
2.320
LEU141
2.496
ASN142
1.857
GLY143
1.852
SER144
3.117
CYS145
2.399
Residue
Distance (Å)
GLY146
4.377
SER147
2.414
VAL148
1.817
PHE150
3.206
ASN151
1.915
ILE152
2.690
ASP153
2.159
TYR154
4.958
ASP155
2.020
CYS156
3.671
VAL157
4.181
SER158
2.385
PHE159
2.959
CYS160
2.331
TYR161
3.675
HIS164
2.073
MET165
2.556
GLU166
1.877
LEU167
2.459
PRO168
2.770
THR169
3.031
GLY170
2.086
VAL171
2.566
HIS172
2.833
ALA173
2.485
GLY174
1.997
THR175
4.606
ASP176
2.278
LEU177
1.785
GLU178
1.785
GLY179
3.829
ASN180
1.695
PHE181
1.855
TYR182
1.895
GLY183
1.907
PRO184
1.937
PHE185
2.136
VAL186
2.522
ASP187
1.922
ARG188
2.380
GLN189
3.631
GLN192
2.854
ALA193
2.702
ALA194
2.000
GLY195
1.837
THR196
2.140
ASP197
2.206
THR198
4.587
THR199
2.325
ILE200
3.418
THR201
2.574
VAL202
2.007
ASN203
1.998
VAL204
2.940
ALA206
3.780
TRP207
2.081
ALA211
4.781
VAL212
1.999
ILE213
3.996
ASN214
2.693
GLY215
2.732
ASP216
2.739
ARG217
2.187
TRP218
2.509
PHE219
2.031
LEU220
4.176
ASN221
3.274
TYR237
2.664
ASN238
2.134
TYR239
1.606
GLU240
2.497
PRO241
3.696
LEU242
3.106
THR243
4.545
HIS246
2.200
ILE249
4.955
SER254
4.781
GLY258
2.852
ILE259
2.436
ALA260
2.204
ASP263
1.632
SER267
2.916
LEU268
4.959
GLU270
2.440
LEU271
2.830
LEU272
3.758
MET276
4.555
ARG279
4.115
THR280
2.050
ILE281
3.474
LEU282
2.737
GLY283
2.166
SER284
2.310
ALA285
2.031
LEU286
2.940
LEU287
2.049
GLU288
1.447
ASP289
1.978
GLU290
2.003
PHE291
2.099
THR292
1.914
PRO293
3.569
PHE294
2.796
ASP295
1.801
VAL296
3.472
ARG298
1.925
GLN299
2.110
CYS300
3.393
VAL303
4.917
THR304
1.968
PHE305
3.534
GLN306
4.624
References  Top
REF 1 Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease. Nat Commun. 2022 Apr 27;13(1):2268.
REF 2 Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography. J Med Chem. 2021 Apr 22;64(8):4991-5000.
REF 3 Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem. 2021 Dec 9;64(23):17366-17383.

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