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 T87325 Target Info
Target Name COVID-19 papain-like proteinase (PL-PRO)
Synonyms COVID-19 papain-like proteinase; COVID-19 PL2-PRO; COVID-19 PL-PRO; COVID-19 main proteinase; COVID-19 non-structural protein 3
Gene Name COVID-19 rep; COVID-19 1a-1b
Biochemical Class Coronaviruses polyprotein 1ab family
UniProt ID
R1AB_SARS2 (819 - 2763)
Ligand General Information  Top
Ligand Name GS-441524 Ligand Info
Canonical SMILES C1=C2C(=NC=NN2C(=C1)C3(C(C(C(O3)CO)O)O)C#N)N
InChI 1S/C12H13N5O4/c13-4-12(10(20)9(19)7(3-18)21-12)8-2-1-6-11(14)15-5-16-17(6)8/h1-2,5,7,9-10,18-20H,3H2,(H2,14,15,16)/t7-,9-,10-,12+/m1/s1
InChIKey BRDWIEOJOWJCLU-LTGWCKQJSA-N
PubChem Compound ID 44468216
Drug Binding Sites of Target  Top
PDB ID: 7QG7      SARS-CoV-2 macrodomain Nsp3b bound to the remdesivir nucleoside GS-441524
Method X-ray diffraction Resolution 1.72 Å Mutation No [1]
PDB Sequence
VNSFSGYLKL
12
TDNVYIKNAD
22
IVEEAKKVKP
32
TVVVNAANVY
42
LKHGGGVAGA
52

LNKATNNAMQ
62
VESDDYIATN
72
GPLKVGGSCV
82
LSGHNLAKHC
92
LHVVGPNVNK
102

GEDIQLLKSA
112
YENFNQHEVL
122
LAPLLSAGIF
132
GADPIHSLRV
142
CVDTVRTNVY
152

LAVFDKNLYD
162
KLVSSFLEMK
172
Residue
Distance (Å)
ALA21
3.730
ASP22
2.702
ILE23
2.958
VAL24
4.674
ALA38
4.670
GLY48
3.910
VAL49
3.456
ALA52
3.848
PRO125
4.284
LEU126
2.480
Residue
Distance (Å)
LEU127
4.332
SER128
4.206
ALA129
3.527
GLY130
3.701
ALA154
3.273
VAL155
3.564
PHE156
3.282
ASP157
3.181
LEU160
3.253
PDB ID: 7BF6      Crystal structure of SARS-CoV-2 macrodomain in complex with remdesivir metabolite GS-441524
Method X-ray diffraction Resolution 2.15 Å Mutation No [2]
PDB Sequence
NSFSGYLKLT
13
DNVYIKNADI
23
VEEAKKVKPT
33
VVVNAANVYL
43
KHGGGVAGAL
53

NKATNNAMQV
63
ESDDYIATNG
73
PLKVGGSCVL
83
SGHNLAKHCL
93
HVVGPNVNKG
103

EDIQLLKSAY
113
ENFNQHEVLL
123
APLLSAGIFG
133
ADPIHSLRVC
143
VDTVRTNVYL
153

AVFDKNLYDK
163
LVSSFLEMK
Residue
Distance (Å)
ALA21
3.808
ASP22
2.661
ILE23
2.980
VAL24
4.784
ALA38
4.420
GLY48
3.910
VAL49
3.389
ALA52
3.886
PRO125
4.194
LEU126
2.911
Residue
Distance (Å)
LEU127
4.640
SER128
4.437
ALA129
3.682
GLY130
4.096
ALA154
3.348
VAL155
3.675
PHE156
3.312
ASP157
3.325
LEU160
3.325
References  Top
REF 1 Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity. J Mol Biol. 2022 Aug 30;434(16):167720.
REF 2 Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain. ACS Med Chem Lett. 2021 Mar 16;12(4):603-609.

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