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,5s)-3-[n-({1-[(Tert-Butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-Methyl-L-Valyl]-N-{(1s)-1-[(1r)-2-(Cyclopropylamino)-1-Hydroxy-2-Oxoethyl]pentyl}-6,6-Dimethyl-3-Azabicyclo[3.1.0]hexane-2-Carboxamide Ligand Info
Canonical SMILES CCCCC(C(C(=O)NC1CC1)O)NC(=O)C2C3C(C3(C)C)CN2C(=O)C(C(C)(C)C)NC(=O)NC4(CCCCC4)CS(=O)(=O)C(C)(C)C
InChI 1S/C36H63N5O7S/c1-10-11-15-24(27(42)30(44)37-22-16-17-22)38-29(43)26-25-23(35(25,8)9)20-41(26)31(45)28(33(2,3)4)39-32(46)40-36(18-13-12-14-19-36)21-49(47,48)34(5,6)7/h22-28,42H,10-21H2,1-9H3,(H,37,44)(H,38,43)(H2,39,40,46)/t23-,24-,25-,26-,27+,28+/m0/s1
InChIKey BZXRATSZUNDEEV-FZFXNXQRSA-N
PubChem Compound ID 52941591
Drug Binding Sites of Target  Top
PDB ID: 7D1O      Crystal structure of SARS-Cov-2 main protease with narlaprevir
Method X-ray diffraction Resolution 1.78 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

S
Residue
Distance (Å)
THR25
3.876
THR26
3.375
LEU27
4.140
HIS41
2.548
MET49
3.645
TYR54
3.841
PHE140
3.822
LEU141
3.495
ASN142
3.610
GLY143
2.842
SER144
3.211
CYS145
1.768
HIS164
3.010
Residue
Distance (Å)
MET165
3.373
GLU166
2.968
LEU167
3.645
PRO168
3.417
PHE185
4.063
VAL186
3.782
ASP187
3.539
ARG188
3.233
GLN189
3.577
THR190
3.076
ALA191
3.552
GLN192
3.469
PDB ID: 7JYC      Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) in Complex with Covalent Inhibitor Narlaprevir
Method X-ray diffraction Resolution 1.79 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)
THR25
3.949
THR26
3.400
LEU27
4.116
HIS41
2.449
MET49
3.617
TYR54
3.807
PHE140
3.173
LEU141
3.652
ASN142
3.633
GLY143
2.856
SER144
3.136
CYS145
1.712
HIS163
4.364
Residue
Distance (Å)
HIS164
2.951
MET165
3.209
GLU166
2.857
LEU167
3.606
PRO168
3.173
PHE185
4.071
VAL186
3.865
ASP187
3.676
ARG188
3.203
GLN189
3.351
THR190
3.274
ALA191
3.520
GLN192
3.366
PDB ID: 6XQT      Room-temperature X-ray Crystal structure of SARS-CoV-2 main protease in complex with Narlaprevir
Method X-ray diffraction Resolution 2.30 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)
THR25
3.893
THR26
3.388
LEU27
4.233
HIS41
2.780
MET49
3.513
TYR54
3.724
PHE140
3.954
LEU141
3.766
ASN142
3.668
GLY143
2.889
SER144
3.431
CYS145
1.836
HIS163
3.956
HIS164
3.047
Residue
Distance (Å)
MET165
3.177
GLU166
2.643
LEU167
3.642
PRO168
3.397
HIS172
4.801
PHE185
3.894
VAL186
3.856
ASP187
3.871
ARG188
3.281
GLN189
3.483
THR190
3.217
ALA191
3.459
GLN192
3.335
References  Top
REF 1 Structural basis for the inhibition of the SARS-CoV-2 main protease by the anti-HCV drug narlaprevir. Signal Transduct Target Ther. 2021 Feb 4;6(1):51.
REF 2 Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep. 2022 Jul 16;12(1):12197.
REF 3 Malleability of the SARS-CoV-2 3CL M(pro) Active-Site Cavity Facilitates Binding of Clinical Antivirals. Structure. 2020 Dec 1;28(12):1313-1320.e3.

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