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-Ethylsuccinimide Ligand Info
Canonical SMILES CCN1C(=O)CCC1=O
InChI 1S/C6H9NO2/c1-2-7-5(8)3-4-6(7)9/h2-4H2,1H3
InChIKey GHAZCVNUKKZTLG-UHFFFAOYSA-N
PubChem Compound ID 16842
Drug Binding Sites of Target  Top
PDB ID: 6XB1      Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design
Method X-ray diffraction Resolution 1.80 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
LNGSGSVGFN
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
TPFDVVRQCS
301

GVTFQ
Residue
Distance (Å)
LYS100
3.487
TYR101
3.225
LYS102
2.572
Residue
Distance (Å)
ASP153
4.573
CYS156
1.799
PDB ID: 6XB2      Room temperature X-ray crystallography reveals catalytic cysteine in the SARS-CoV-2 3CL Mpro is highly reactive: Insights for enzyme mechanism and drug design
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

SGVTFQ
Residue
Distance (Å)
THR25
4.162
THR26
3.819
LEU27
4.709
HIS41
3.498
LYS100
3.932
TYR101
4.511
LYS102
3.239
Residue
Distance (Å)
ASN142
4.115
GLY143
3.616
SER144
4.171
CYS145
1.794
CYS156
1.803
HIS164
4.110
References  Top
REF 1 Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M(pro): insights into enzyme mechanism and drug design. IUCrJ. 2020 Sep 21;7(Pt 6):1028-35.

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