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 4-{2-(4-Fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo-heptanoylamino}-5-(2-oxo-pyrrolidin-3-YL)-pentanoic acid ethyl ester Ligand Info
Canonical SMILES CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(CC2=CC=C(C=C2)F)CC(=O)C(C(C)C)NC(=O)C3=NOC(=C3)C
InChI 1S/C31H41FN4O7/c1-5-42-27(38)11-10-24(16-21-12-13-33-29(21)39)34-30(40)22(15-20-6-8-23(32)9-7-20)17-26(37)28(18(2)3)35-31(41)25-14-19(4)43-36-25/h6-9,14,18,21-22,24,28H,5,10-13,15-17H2,1-4H3,(H,33,39)(H,34,40)(H,35,41)/t21-,22+,24+,28-/m0/s1
InChIKey LMIUALQNZXJHOG-IFILWLFVSA-N
PubChem Compound ID 6323208
Drug Binding Sites of Target  Top
PDB ID: 7L8I      SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21)
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
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

SGVTF
Residue
Distance (Å)
THR24
4.977
THR25
2.179
THR26
2.469
LEU27
2.405
PRO39
2.438
HIS41
2.496
VAL42
4.283
MET49
2.624
PHE140
2.719
LEU141
3.022
ASN142
2.348
GLY143
2.522
SER144
2.524
CYS145
1.766
Residue
Distance (Å)
HIS163
2.013
HIS164
1.912
MET165
2.362
GLU166
1.950
LEU167
2.756
PRO168
2.400
HIS172
2.657
ASP187
3.779
ARG188
4.432
GLN189
3.099
THR190
3.285
ALA191
3.461
GLN192
2.697
ALA193
4.859
PDB ID: 7L8J      SARS-CoV-2 Main Protease (Mpro) in Complex with Rupintrivir (P21212)
Method X-ray diffraction Resolution 2.45 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

SGVTF
Residue
Distance (Å)
THR25
3.702
THR26
4.464
LEU27
2.358
PRO39
2.485
HIS41
2.399
VAL42
4.198
SER46
4.942
MET49
4.400
PHE140
2.738
LEU141
2.786
ASN142
2.291
GLY143
2.290
SER144
2.588
CYS145
1.771
HIS163
2.355
HIS164
1.929
Residue
Distance (Å)
MET165
2.271
GLU166
2.038
LEU167
3.162
PRO168
2.583
HIS172
2.906
ALA173
4.526
PHE185
2.964
VAL186
3.724
ASP187
3.884
ARG188
3.524
GLN189
2.382
THR190
3.195
ALA191
3.827
GLN192
2.615
ALA193
4.916
References  Top
REF 1 Pan-3C Protease Inhibitor Rupintrivir Binds SARS-CoV-2 Main Protease in a Unique Binding Mode. Biochemistry. 2021 Oct 5;60(39):2925-2931.

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