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: 7TX0      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)
Method X-ray diffraction Resolution 0.84 Å Mutation No [1]
PDB Sequence
SFSGYLKLTD
14
NVYIKNADIV
24
EEAKKVKPTV
34
VVNAANVYLK
44
HGGGVAGALN
54

KATNNAMQVE
64
SDDYIATNGP
74
LKVGGSCVLS
84
GHNLAKHCLH
94
VVGPNVNKGE
104

DIQLLKSAYE
114
NFNQHEVLLA
124
PLLSAGIFGA
134
DPIHSLRVCV
144
DTVRTNVYLA
154

VFDKNLYDKL
164
VSSFL
Residue
Distance (Å)
ALA21
3.265
ASP22
2.686
ILE23
2.107
VAL24
3.054
ASN37
4.339
ALA38
2.503
ALA39
3.046
ASN40
1.993
LYS44
3.092
HIS45
2.518
GLY46
2.888
GLY47
2.156
GLY48
2.699
VAL49
2.026
ALA50
2.465
GLY51
3.721
ALA52
2.909
Residue
Distance (Å)
GLY97
4.630
PRO125
3.382
LEU126
2.632
LEU127
3.571
SER128
2.042
ALA129
2.534
GLY130
2.049
ILE131
2.174
PHE132
2.257
GLY133
4.101
PRO136
3.807
ALA154
2.674
VAL155
3.795
PHE156
2.612
ASP157
3.896
LEU160
3.328
PDB ID: 7KQP      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal form)
Method X-ray diffraction Resolution 0.88 Å Mutation No [2]
PDB Sequence
SMVNSFSGYL
10
KLTDNVYIKN
20
ADIVEEAKKV
30
KPTVVVNAAN
40
VYLKHGGGVA
50

GALNKATNNA
60
MQVESDDYIA
70
TNGPLKVGGS
80
CVLSGHNLAK
90
HCLHVVGPNV
100

NKGEDIQLLK
110
SAYENFNQHE
120
VLLAPLLSAG
130
IFGADPIHSL
140
RVCVDTVRTN
150

VYLAVFDKNL
160
YDKLVSSFL
Residue
Distance (Å)
ALA21
3.315
ASP22
2.807
ILE23
2.100
VAL24
3.102
ASN37
4.370
ALA38
2.535
ALA39
3.054
ASN40
2.011
LYS44
3.148
HIS45
2.418
GLY46
2.851
GLY47
2.186
GLY48
2.676
VAL49
2.034
ALA50
2.338
GLY51
3.663
ALA52
2.892
Residue
Distance (Å)
GLY97
4.631
PRO125
3.382
LEU126
2.682
LEU127
3.625
SER128
2.043
ALA129
2.552
GLY130
2.043
ILE131
2.197
PHE132
2.241
GLY133
4.095
PRO136
3.868
ALA154
2.681
VAL155
3.816
PHE156
2.609
ASP157
3.903
LEU160
3.363
PDB ID: 7TWT      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 4 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [3]
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)
ALA21
3.280
ASP22
2.737
ILE23
2.130
VAL24
3.181
ASN37
4.377
ALA38
2.532
ALA39
3.068
ASN40
2.004
LYS44
3.035
HIS45
2.467
GLY46
2.782
GLY47
2.097
GLY48
2.689
VAL49
2.038
ALA50
2.527
GLY51
3.788
ALA52
2.885
Residue
Distance (Å)
GLY97
4.637
PRO125
3.324
LEU126
2.626
LEU127
3.578
SER128
2.040
ALA129
2.494
GLY130
2.067
ILE131
2.182
PHE132
2.249
GLY133
4.122
PRO136
3.822
ALA154
2.672
VAL155
3.810
PHE156
2.632
ASP157
3.982
LEU160
3.394
PDB ID: 7TWV      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [4]
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
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .A:21 or .A:22 or .A:23 or .A:24 or .A:37 or .A:38 or .A:39 or .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:97 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:136 or .A:154 or .A:155 or .A:156 or .A:157 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA21
3.277
ASP22
2.706
ILE23
2.117
VAL24
3.097
ASN37
4.378
ALA38
2.523
ALA39
3.061
ASN40
1.995
LYS44
3.217
HIS45
2.402
GLY46
2.804
GLY47
2.097
GLY48
2.679
VAL49
2.027
ALA50
2.267
GLY51
3.748
ALA52
2.906
Residue
Distance (Å)
GLY97
4.617
PRO125
3.321
LEU126
2.633
LEU127
3.541
SER128
2.014
ALA129
2.507
GLY130
2.046
ILE131
2.169
PHE132
2.253
GLY133
4.104
PRO136
3.830
ALA154
2.669
VAL155
3.810
PHE156
2.611
ASP157
3.927
LEU160
3.361
PDB ID: 7TWW      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 6 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [5]
PDB Sequence
MVNSFSGYLK
11
LTDNVYIKNA
21
DIVEEAKKVK
31
PTVVVNAANV
41
YLKHGGGVAG
51

ALNKATNNAM
61
QVESDDYIAT
71
NGPLKVGGSC
81
VLSGHNLAKH
91
CLHVVGPNVN
101

KGEDIQLLKS
111
AYENFNQHEV
121
LLAPLLSAGI
131
FGADPIHSLR
141
VCVDTVRTNV
151

YLAVFDKNLY
161
DKLVSSFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .A:21 or .A:22 or .A:23 or .A:24 or .A:37 or .A:38 or .A:39 or .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:97 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:136 or .A:154 or .A:155 or .A:156 or .A:157 or .A:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA21
3.273
ASP22
2.732
ILE23
2.113
VAL24
2.996
ASN37
4.330
ALA38
2.516
ALA39
3.048
ASN40
1.981
LYS44
3.067
HIS45
2.467
GLY46
2.854
GLY47
2.312
GLY48
2.690
VAL49
2.035
ALA50
2.393
GLY51
3.762
ALA52
2.944
Residue
Distance (Å)
GLY97
4.612
PRO125
3.341
LEU126
2.634
LEU127
3.530
SER128
2.006
ALA129
2.529
GLY130
2.048
ILE131
2.164
PHE132
2.253
GLY133
4.091
PRO136
3.859
ALA154
2.654
VAL155
3.801
PHE156
2.603
ASP157
3.905
LEU160
3.340
PDB ID: 7TWX      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 7 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [6]
PDB Sequence
MVNSFSGYLK
11
LTDNVYIKNA
21
DIVEEAKKVK
31
PTVVVNAANV
41
YLKHGGGVAG
51

ALNKATNNAM
61
QVESDDYIAT
71
NGPLKVGGSC
81
VLSGHNLAKH
91
CLHVVGPNVN
101

KGEDIQLLKS
111
AYENFNQHEV
121
LLAPLLSAGI
131
FGADPIHSLR
141
VCVDTVRTNV
151

YLAVFDKNLY
161
DKLVSSFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .A:21 or .A:22 or .A:23 or .A:24 or .A:37 or .A:38 or .A:39 or .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:97 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:136 or .A:154 or .A:155 or .A:156 or .A:157 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA21
3.270
ASP22
2.613
ILE23
2.110
VAL24
3.081
ASN37
4.324
ALA38
2.508
ALA39
3.046
ASN40
1.984
LYS44
3.108
HIS45
2.475
GLY46
2.876
GLY47
2.343
GLY48
2.701
VAL49
2.042
ALA50
2.370
GLY51
3.771
ALA52
2.868
Residue
Distance (Å)
GLY97
4.623
PRO125
3.361
LEU126
2.637
LEU127
3.549
SER128
2.027
ALA129
2.403
GLY130
2.043
ILE131
2.163
PHE132
2.256
GLY133
4.100
PRO136
3.821
ALA154
2.652
VAL155
3.800
PHE156
2.620
ASP157
3.902
LEU160
3.359
PDB ID: 7TWY      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 8 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [7]
PDB Sequence
MVNSFSGYLK
11
LTDNVYIKNA
21
DIVEEAKKVK
31
PTVVVNAANV
41
YLKHGGGVAG
51

ALNKATNNAM
61
QVESDDYIAT
71
NGPLKVGGSC
81
VLSGHNLAKH
91
CLHVVGPNVN
101

KGEDIQLLKS
111
AYENFNQHEV
121
LLAPLLSAGI
131
FGADPIHSLR
141
VCVDTVRTNV
151

YLAVFDKNLY
161
DKLVSSFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .A:21 or .A:22 or .A:23 or .A:24 or .A:37 or .A:38 or .A:39 or .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:97 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:136 or .A:154 or .A:155 or .A:156 or .A:157 or .A:160; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA21
3.266
ASP22
2.713
ILE23
2.108
VAL24
3.020
ASN37
4.336
ALA38
2.514
ALA39
3.034
ASN40
1.984
LYS44
3.162
HIS45
2.442
GLY46
2.880
GLY47
2.395
GLY48
2.696
VAL49
2.036
ALA50
2.266
GLY51
3.755
ALA52
2.928
Residue
Distance (Å)
GLY97
4.622
PRO125
3.367
LEU126
2.643
LEU127
3.561
SER128
2.030
ALA129
2.523
GLY130
2.046
ILE131
2.169
PHE132
2.251
GLY133
4.100
PRO136
3.829
ALA154
2.649
VAL155
3.800
PHE156
2.612
ASP157
3.892
LEU160
3.330
PDB ID: 7TX1      Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 10 (P43 crystal form)
Method X-ray diffraction Resolution 0.90 Å Mutation No [8]
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
LVSSFL
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .A:21 or .A:22 or .A:23 or .A:24 or .A:37 or .A:38 or .A:39 or .A:40 or .A:44 or .A:45 or .A:46 or .A:47 or .A:48 or .A:49 or .A:50 or .A:51 or .A:52 or .A:97 or .A:125 or .A:126 or .A:127 or .A:128 or .A:129 or .A:130 or .A:131 or .A:132 or .A:133 or .A:136 or .A:154 or .A:155 or .A:156 or .A:157 or .A:160; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ALA21
3.257
ASP22
2.680
ILE23
2.097
VAL24
3.056
ASN37
4.346
ALA38
2.505
ALA39
3.048
ASN40
1.996
LYS44
3.156
HIS45
2.515
GLY46
2.895
GLY47
2.158
GLY48
2.708
VAL49
2.023
ALA50
2.451
GLY51
3.707
ALA52
2.916
Residue
Distance (Å)
GLY97
4.631
PRO125
3.375
LEU126
2.657
LEU127
3.578
SER128
2.042
ALA129
2.569
GLY130
2.050
ILE131
2.179
PHE132
2.253
GLY133
4.098
PRO136
3.818
ALA154
2.677
VAL155
3.799
PHE156
2.606
ASP157
3.901
LEU160
3.318
References  Top
REF 1 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43 crystal form)
REF 2 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 Apr 14;7(16):eabf8711.
REF 3 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 4 (P43 crystal form)
REF 4 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)
REF 5 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 6 (P43 crystal form)
REF 6 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 7 (P43 crystal form)
REF 7 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 8 (P43 crystal form)
REF 8 Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 10 (P43 crystal form)

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