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 N-[(2S)-1-[[(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide Ligand Info
Canonical SMILES CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C2=NC3=CC=CC=C3S2)O)NC(=O)C4=CC5=C(N4)C=CC=C5OC
InChI 1S/C30H35N5O5S/c1-16(2)13-22(34-29(39)23-15-18-19(32-23)8-6-9-24(18)40-3)28(38)33-21(14-17-11-12-31-27(17)37)26(36)30-35-20-7-4-5-10-25(20)41-30/h4-10,15-17,21-22,26,32,36H,11-14H2,1-3H3,(H,31,37)(H,33,38)(H,34,39)/t17-,21-,22-,26-/m0/s1
InChIKey DHQWCSDZTRDSRP-XIBGDNMGSA-N
PubChem Compound ID 154573806
Drug Binding Sites of Target  Top
PDB ID: 7JKV      Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420
Method X-ray diffraction Resolution 1.25 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
3.504
LEU27
4.102
HIS41
3.102
VAL42
4.750
CYS44
4.307
MET49
3.520
TYR54
4.646
PHE140
3.141
LEU141
3.672
ASN142
3.186
GLY143
3.421
SER144
3.416
CYS145
1.865
Residue
Distance (Å)
HIS163
2.706
HIS164
2.873
MET165
3.319
GLU166
2.694
LEU167
4.440
PRO168
3.775
HIS172
3.462
ASP187
3.883
ARG188
3.967
GLN189
2.932
THR190
3.526
ALA191
3.593
PDB ID: 6XR3      X-ray Structure of SARS-CoV-2 main protease bound to GRL-024-20 at 1.45 A
Method X-ray diffraction Resolution 1.45 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

SGVTF
Residue
Distance (Å)
THR25
2.698
LEU27
3.314
PRO39
4.733
HIS41
2.559
VAL42
3.598
CYS44
3.090
MET49
3.012
LEU50
4.737
PRO52
4.986
TYR54
3.811
PHE140
2.948
LEU141
3.371
ASN142
2.275
GLY143
2.740
SER144
2.660
CYS145
1.763
Residue
Distance (Å)
HIS163
1.814
HIS164
2.061
MET165
2.322
GLU166
1.659
LEU167
3.466
PRO168
2.210
HIS172
2.903
PHE181
4.382
VAL186
4.206
ASP187
2.377
ARG188
2.765
GLN189
2.142
THR190
2.571
ALA191
2.603
GLN192
4.621
References  Top
REF 1 A small molecule?compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun. 2021 Jan 28;12(1):668.
REF 2 X-ray Structure of SARS-CoV-2 main protease bound to GRL-024-20 at 1.45 A

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