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 (1R,2R)-1-[4-(cyclopropylcarbamamido)benzamido]-4-hydroxy-2,3-dihydro-1H-indene-2-carboxylic acid Ligand Info
Canonical SMILES C1CC1NC(=O)NC2=CC=C(C=C2)C(=O)NC3C(CC4=C3C=CC=C4O)C(=O)O
InChI 1S/C21H21N3O5/c25-17-3-1-2-14-15(17)10-16(20(27)28)18(14)24-19(26)11-4-6-12(7-5-11)22-21(29)23-13-8-9-13/h1-7,13,16,18,25H,8-10H2,(H,24,26)(H,27,28)(H2,22,23,29)/t16-,18+/m1/s1
InChIKey HULQKGAWTDMSSA-AEFFLSMTSA-N
PubChem Compound ID 164513220
Drug Binding Sites of Target  Top
PDB ID: 5SPD      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398539 - (R,R) and (S,S) isomers
Method X-ray diffraction Resolution 1.05 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
KLVSSFL
Residue
Distance (Å)
ASP22
1.958
ILE23
2.759
VAL24
2.693
GLU25
4.059
ALA38
2.491
GLY47
4.797
GLY48
2.459
VAL49
2.508
ALA50
4.731
ALA52
2.535
LYS55
4.002
PRO125
2.873
Residue
Distance (Å)
LEU126
2.200
LEU127
3.294
SER128
3.078
ALA129
2.090
GLY130
2.636
ILE131
2.103
PHE132
2.682
ALA154
3.880
VAL155
3.081
PHE156
2.343
ASP157
3.054
LEU160
3.801
PDB ID: 5SQJ      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5021668601
Method X-ray diffraction Resolution 1.05 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
KLVSSFL
Residue
Distance (Å)
ASP22
2.003
ILE23
2.673
VAL24
2.890
GLU25
3.771
LYS28
4.660
ALA38
2.734
GLY47
4.804
GLY48
2.304
VAL49
2.868
ALA50
4.909
ALA52
2.670
LYS55
4.430
PRO125
2.994
Residue
Distance (Å)
LEU126
2.669
LEU127
2.923
SER128
2.510
ALA129
2.378
GLY130
2.711
ILE131
2.650
PHE132
2.678
ALA154
4.031
VAL155
2.877
PHE156
1.939
ASP157
2.276
LEU160
3.026
References  Top
REF 1 Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv. 2022 Jul 28:2022.06.27.497816.

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