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 (1S,2S)-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+/m0/s1
InChIKey HULQKGAWTDMSSA-FUHWJXTLSA-N
PubChem Compound ID 164513219
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
1.957
ILE23
2.755
VAL24
2.679
GLU25
4.052
GLY48
2.413
VAL49
2.520
ALA52
2.527
LYS55
3.999
PRO125
2.981
LEU126
3.671
Residue
Distance (Å)
ALA129
2.539
GLY130
1.960
ILE131
3.759
PRO136
2.933
ALA154
3.745
VAL155
3.035
PHE156
2.354
ASP157
2.961
LEU160
2.393
PDB ID: 5SR3      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5021669050 - (S,S) isomer
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
2.026
ILE23
2.613
VAL24
2.830
GLU25
3.857
LYS28
4.723
GLY48
2.427
VAL49
2.736
ALA52
2.583
LYS55
4.448
PRO125
3.171
Residue
Distance (Å)
LEU126
3.797
ALA129
2.791
GLY130
2.058
ILE131
3.986
PRO136
3.417
ALA154
4.113
VAL155
2.866
PHE156
2.045
ASP157
2.768
LEU160
2.261
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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