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-[(Benzyloxy)carbonyl]-O-(Tert-Butyl)-L-Threonyl-3-Cyclohexyl-N-[(1s)-2-Hydroxy-1-{[(3s)-2-Oxopyrrolidin-3-Yl]methyl}ethyl]-L-Alaninamide Ligand Info
Canonical SMILES CC(C(C(=O)NC(CC1CCCCC1)C(=O)NC(CC2CCNC2=O)CO)NC(=O)OCC3=CC=CC=C3)OC(C)(C)C
InChI 1S/C32H50N4O7/c1-21(43-32(2,3)4)27(36-31(41)42-20-23-13-9-6-10-14-23)30(40)35-26(17-22-11-7-5-8-12-22)29(39)34-25(19-37)18-24-15-16-33-28(24)38/h6,9-10,13-14,21-22,24-27,37H,5,7-8,11-12,15-20H2,1-4H3,(H,33,38)(H,34,39)(H,35,40)(H,36,41)/t21-,24+,25+,26+,27+/m1/s1
InChIKey YIWYOEOSWRXENJ-FFXRMZKPSA-N
PubChem Compound ID 11844232
Drug Binding Sites of Target  Top
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
Residue
Distance (Å)
LEU27
4.995
HIS41
3.415
CYS44
4.369
MET49
3.332
PRO52
4.859
TYR54
3.549
PHE140
3.030
LEU141
3.652
ASN142
2.946
GLY143
2.929
SER144
3.507
CYS145
1.789
HIS163
2.860
Residue
Distance (Å)
HIS164
3.073
MET165
3.093
GLU166
2.561
LEU167
4.189
PRO168
3.183
HIS172
3.801
ASP187
3.133
ARG188
3.586
GLN189
3.271
THR190
2.736
ALA191
3.551
GLN192
3.903
PDB ID: 7C8T      Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221
Method X-ray diffraction Resolution 2.05 Å Mutation No [2]
PDB Sequence
SGFRKMAFPS
10
GKVEGCMVQV
20
TCTTLNGLWL
32
DDVVYCPRHV
42
ICMLNPNYED
56

LLIRKSNHNF
66
LVQAGNVQLR
76
VIGHSMQNCV
86
LKLKVDTANP
96
KTPKYKFVRI
106

QPGQTFSVLA
116
CYNGSPSGVY
126
QCAMRPNFTI
136
KGSFLNGSCG
146
SVGFNIDYDC
156

VSFCYMHHME
166
LPTGVHAGTD
176
LEGNFYGPFV
186
DRQTAQAAGT
196
DTTITVNVLA
206

WLYAAVINGD
216
RWFLNRFTTT
226
LNDFNLVAMK
236
YNYEPLTQDH
246
VDILGPLSAQ
256

TGIAVLDMCA
266
SLKELLQNGM
276
NGRTILGSAL
286
LEDEFTPFDV
296
VRQCSGVTFQ
306
Residue
Distance (Å)
LEU27
4.839
HIS41
3.576
CYS44
3.848
MET49
3.850
TYR54
3.775
PHE140
3.376
LEU141
3.750
ASN142
3.289
GLY143
3.096
SER144
3.361
CYS145
1.701
HIS163
2.685
Residue
Distance (Å)
HIS164
3.272
MET165
3.347
GLU166
2.706
LEU167
3.701
PRO168
3.797
HIS172
3.574
ASP187
3.485
ARG188
3.664
GLN189
3.407
THR190
3.141
ALA191
3.634
GLN192
3.427
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 Complex Structure of SARS-CoV-2 3CL Protease with TG-0205221

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