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 Adenosine-5-diphosphoribose Ligand Info
Canonical SMILES C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
InChI 1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKey SRNWOUGRCWSEMX-ZQSHOCFMSA-N
PubChem Compound ID 447048
Drug Binding Sites of Target  Top
PDB ID: 6Z5T      SARS-CoV-2 Macrodomain in complex with ADP-ribose
Method X-ray diffraction Resolution 1.57 Å Mutation No [1]
PDB Sequence
EVNSFSGYLK
215
LTDNVYIKNA
225
DIVEEAKKVK
235
PTVVVNAANV
245
YLKHGGGVAG
255

ALNKATNNAM
265
QVESDDYIAT
275
NGPLKVGGSC
285
VLSGHNLAKH
295
CLHVVGPNVN
305

KGEDIQLLKS
315
AYENFNQHEV
325
LLAPLLSAGI
335
FGADPIHSLR
345
VCVDTVRTNV
355

YLAVFDKNLY
365
DKLVSSFLEM
375
KSEK
Residue
Distance (Å)
ALA225
4.000
ASP226
2.837
ILE227
2.948
VAL228
4.953
ALA242
3.510
ALA243
4.069
ASN244
2.810
LYS248
3.195
HIS249
3.645
GLY250
2.950
GLY251
3.509
GLY252
2.895
VAL253
2.790
ALA254
3.616
GLY255
4.365
Residue
Distance (Å)
ALA256
4.039
PRO329
3.984
LEU330
3.157
LEU331
4.048
SER332
2.868
ALA333
3.243
GLY334
2.705
ILE335
2.776
PHE336
2.999
GLY337
4.516
ALA358
3.509
VAL359
4.614
PHE360
3.332
LEU364
4.042
PDB ID: 6WOJ      Structure of the SARS-CoV-2 macrodomain (NSP3) in complex with ADP-ribose
Method X-ray diffraction Resolution 2.20 Å Mutation No [2]
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
KLVSSFLEM
Residue
Distance (Å)
ALA21
4.017
ASP22
2.938
ILE23
3.039
VAL24
4.959
ALA38
3.486
ALA39
4.130
ASN40
2.767
LYS44
3.122
HIS45
3.799
GLY46
3.234
GLY47
3.339
GLY48
2.989
VAL49
2.786
ALA50
3.471
GLY51
4.246
Residue
Distance (Å)
ALA52
4.230
PRO125
3.829
LEU126
3.231
LEU127
4.114
SER128
2.925
ALA129
3.277
GLY130
2.848
ILE131
2.903
PHE132
2.832
GLY133
4.390
ALA154
3.500
VAL155
4.604
PHE156
3.599
LEU160
3.826
PDB ID: 6YWL      Crystal structure of SARS-CoV-2 (Covid-19) NSP3 macrodomain in complex with ADP-ribose
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
GHMVNSFSGY
9
LKLTDNVYIK
19
NADIVEEAKK
29
VKPTVVVNAA
39
NVYLKHGGGV
49

AGALNKATNN
59
AMQVESDDYI
69
ATNGPLKVGG
79
SCVLSGHNLA
89
KHCLHVVGPN
99

VNKGEDIQLL
109
KSAYENFNQH
119
EVLLAPLLSA
129
GIFGADPIHS
139
LRVCVDTVRT
149

NVYLAVFDKN
159
LYDKLVSSFL
169
EM
Residue
Distance (Å)
ALA21
3.758
ASP22
2.737
ILE23
3.017
VAL24
4.932
ALA38
3.475
ALA39
4.013
ASN40
2.844
LYS44
3.033
HIS45
3.706
GLY46
3.258
GLY47
2.397
GLY48
3.420
VAL49
2.798
ALA50
3.451
GLY51
4.479
Residue
Distance (Å)
ALA52
4.111
PRO125
3.949
LEU126
3.086
LEU127
4.087
SER128
2.919
ALA129
3.335
GLY130
2.822
ILE131
2.821
PHE132
2.952
GLY133
4.432
ALA154
3.358
VAL155
4.184
PHE156
3.505
LEU160
3.768
PDB ID: 6W02      Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with ADP ribose
Method X-ray diffraction Resolution 1.50 Å Mutation No [4]
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
LVSSF
Click to Show 3D Structure of This Binding Site
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Residue
Distance (Å)
ALA21
3.704
ASP22
2.919
ILE23
2.933
VAL24
4.933
ALA38
3.431
ALA39
4.074
ASN40
2.948
LYS44
2.984
HIS45
3.754
GLY46
2.973
GLY47
3.414
GLY48
2.914
VAL49
2.780
ALA50
3.734
GLY51
4.561
Residue
Distance (Å)
ALA52
4.115
PRO125
4.014
LEU126
3.035
LEU127
4.050
SER128
2.870
ALA129
3.331
GLY130
2.769
ILE131
2.868
PHE132
2.978
GLY133
4.545
ALA154
3.341
VAL155
4.030
PHE156
3.423
ASP157
4.973
LEU160
3.563
References  Top
REF 1 Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential. Open Biol. 2020 Nov;10(11):200237.
REF 2 The SARS-CoV-2 Conserved Macrodomain Is a Mono-ADP-Ribosylhydrolase. J Virol. 2021 Jan 13;95(3):e01969-20.
REF 3 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.
REF 4 Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes. IUCrJ. 2020 Jul 17;7(Pt 5):814-824.

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