Receptor
PDB id Resolution Class Description Source Keywords
5VSM 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VIPERIN WITH BOUND [4FE-4S] CLUSTER, 5' DEOXYADENOSINE, AND L-METHIONINE MUS MUSCULUS RADICAL S-ADENOSYLMETHIONINE IRON-SULFUR CLUSTER ANTIVIRARESPONSE ANTIVIRAL PROTEIN
Ref.: STRUCTURAL STUDIES OF VIPERIN, AN ANTIVIRAL RADICAL ENZYME. PROC. NATL. ACAD. SCI. V. 114 6806 2017 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5AD A:402;
B:402;
Valid;
Valid;
none;
none;
submit data
251.242 C10 H13 N5 O3 C[C@@...
MET A:403;
B:403;
Valid;
Valid;
none;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
SF4 A:401;
B:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VSM 1.7 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VIPERIN WITH BOUND [4FE-4S] CLUSTER, 5' DEOXYADENOSINE, AND L-METHIONINE MUS MUSCULUS RADICAL S-ADENOSYLMETHIONINE IRON-SULFUR CLUSTER ANTIVIRARESPONSE ANTIVIRAL PROTEIN
Ref.: STRUCTURAL STUDIES OF VIPERIN, AN ANTIVIRAL RADICAL ENZYME. PROC. NATL. ACAD. SCI. V. 114 6806 2017 U.S.A.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5VSM - MET C5 H11 N O2 S CSCC[C@@H]....
2 5VSL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5VSM - MET C5 H11 N O2 S CSCC[C@@H]....
2 5VSL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5VSM - MET C5 H11 N O2 S CSCC[C@@H]....
2 5VSL - SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5AD; Similar ligands found: 196
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD 1 1
2 XYA 0.672727 0.854839
3 ADN 0.672727 0.854839
4 RAB 0.672727 0.854839
5 5N5 0.649123 0.854839
6 Y3J 0.649123 0.929825
7 MTA 0.639344 0.857143
8 5CD 0.637931 0.868852
9 A4D 0.637931 0.854839
10 EP4 0.633333 0.830769
11 M2T 0.622951 0.80597
12 DTA 0.596774 0.815385
13 3DH 0.59375 0.857143
14 CC5 0.568965 0.883333
15 7D7 0.568965 0.793651
16 S4M 0.565217 0.72
17 NEC 0.558824 0.885246
18 AOC 0.558824 0.828125
19 AMP 0.552239 0.768116
20 ZAS 0.552239 0.791045
21 A 0.552239 0.768116
22 A3N 0.550725 0.815385
23 ABM 0.550725 0.771429
24 SRA 0.544118 0.726027
25 6RE 0.544118 0.757143
26 3AM 0.537313 0.753623
27 AMP MG 0.536232 0.746479
28 DSH 0.536232 0.768116
29 MAO 0.535211 0.710526
30 3AD 0.532258 0.83871
31 RP1 0.529412 0.722222
32 SP1 0.529412 0.722222
33 J7C 0.528571 0.768116
34 A2D 0.528571 0.746479
35 5AS 0.527778 0.650602
36 GJV 0.521127 0.746479
37 SON 0.520548 0.716216
38 A3G 0.514286 0.80303
39 AP2 0.513889 0.716216
40 BA3 0.513889 0.746479
41 A12 0.513889 0.716216
42 AU1 0.513514 0.726027
43 M33 0.513514 0.760563
44 MHZ 0.513514 0.710526
45 ADP 0.506849 0.746479
46 B4P 0.506849 0.746479
47 AP5 0.506849 0.746479
48 A7D 0.5 0.80303
49 AN2 0.5 0.736111
50 SAM 0.5 0.75
51 PRX 0.5 0.75
52 2AM 0.5 0.742857
53 SA8 0.493506 0.771429
54 AD9 0.493506 0.726027
55 CA0 0.493333 0.726027
56 ADP MG 0.493333 0.736111
57 ADX 0.493333 0.670886
58 CMP 0.493151 0.776119
59 A3P 0.493151 0.742857
60 2BA 0.493151 0.764706
61 ACP 0.486842 0.726027
62 BEF ADP 0.486842 0.716216
63 SFG 0.486842 0.828125
64 5X8 0.486842 0.815385
65 ATP 0.486842 0.746479
66 50T 0.486842 0.736111
67 A3T 0.486842 0.857143
68 ADP BEF 0.486842 0.716216
69 7D5 0.485294 0.684932
70 SMM 0.481481 0.72
71 ANP 0.481013 0.726027
72 AR6 0.480519 0.746479
73 5FA 0.480519 0.746479
74 AQP 0.480519 0.746479
75 APC 0.480519 0.716216
76 APR 0.480519 0.746479
77 A3S 0.48 0.815385
78 OVE 0.478873 0.712329
79 5AL 0.475 0.760563
80 EEM 0.475 0.75
81 AAT 0.475 0.746479
82 SAP 0.474359 0.706667
83 RBY 0.474359 0.716216
84 ADV 0.474359 0.716216
85 A5D 0.474359 0.815385
86 ADP PO3 0.474359 0.768116
87 AGS 0.474359 0.706667
88 QQX 0.471429 0.708333
89 5F1 0.469697 0.78125
90 A5A 0.469136 0.675
91 SAI 0.468354 0.779412
92 ATP MG 0.468354 0.736111
93 G5A 0.468354 0.630952
94 SAH 0.468354 0.791045
95 QQY 0.464789 0.71831
96 103 0.464789 0.764706
97 ACK 0.464789 0.761194
98 S7M 0.463415 0.75
99 ANP MG 0.463415 0.706667
100 GAP 0.4625 0.726027
101 TAT 0.4625 0.716216
102 ACQ 0.4625 0.726027
103 3L1 0.461538 0.772727
104 3D1 0.461538 0.772727
105 VMS 0.457831 0.658537
106 54H 0.457831 0.658537
107 52H 0.457831 0.650602
108 PAP 0.455696 0.732394
109 NVA 2AD 0.455696 0.791045
110 A2P 0.453333 0.753623
111 NOC 0.453125 0.790323
112 5I5 0.453125 0.913793
113 MAP 0.452381 0.706667
114 DAL AMP 0.452381 0.760563
115 53H 0.452381 0.650602
116 TSB 0.452381 0.666667
117 ATF 0.451219 0.716216
118 ALF ADP 0.451219 0.706667
119 ADP ALF 0.451219 0.706667
120 2VA 0.448718 0.830769
121 5SV 0.447059 0.710526
122 8QN 0.447059 0.760563
123 SSA 0.445783 0.630952
124 SRP 0.445783 0.716216
125 ADP VO4 0.445783 0.736111
126 VO4 ADP 0.445783 0.736111
127 LSS 0.44186 0.635294
128 PAJ 0.44186 0.701299
129 0UM 0.44186 0.760563
130 7D3 0.44 0.666667
131 PPS 0.439024 0.65
132 1ZZ 0.438202 0.683544
133 NVA LMS 0.436782 0.635294
134 62X 0.436782 0.72
135 A22 0.435294 0.736111
136 5CA 0.435294 0.630952
137 D3Y 0.435294 0.791045
138 KB1 0.433333 0.736111
139 MYR AMP 0.433333 0.683544
140 ARJ 0.432836 0.774194
141 VRT 0.432099 0.794118
142 SO8 0.432099 0.818182
143 OAD 0.431818 0.75
144 K15 0.431818 0.739726
145 LEU LMS 0.431818 0.635294
146 25A 0.430233 0.746479
147 GEK 0.430233 0.757143
148 S8M 0.430233 0.757143
149 OOB 0.430233 0.736111
150 WAQ 0.426966 0.697368
151 3NZ 0.426966 0.782609
152 GSU 0.426966 0.630952
153 ADZ 0.425926 0.618182
154 DSZ 0.425287 0.630952
155 ADQ 0.425287 0.726027
156 4AD 0.425287 0.706667
157 AMO 0.425287 0.716216
158 NSS 0.425287 0.630952
159 A1R 0.425287 0.697368
160 2A5 0.425 0.68
161 TXA 0.422222 0.739726
162 SXZ 0.422222 0.75
163 3OD 0.422222 0.75
164 ME8 0.422222 0.683544
165 PTJ 0.422222 0.710526
166 BIS 0.422222 0.697368
167 AHX 0.420455 0.688312
168 DLL 0.420455 0.736111
169 00A 0.420455 0.697368
170 ATR 0.419753 0.742857
171 7D4 0.417722 0.666667
172 TAD 0.416667 0.679487
173 A6D 0.41573 0.716216
174 ADP BMA 0.41573 0.726027
175 3UK 0.41573 0.726027
176 26A 0.411765 0.787879
177 AFX 0.411765 0.716418
178 P5A 0.411111 0.602273
179 LAD 0.411111 0.679487
180 PR8 0.411111 0.670886
181 A A 0.411111 0.746479
182 KAA 0.411111 0.609195
183 V3L 0.409639 0.746479
184 AMP NAD 0.409091 0.739726
185 YAP 0.408602 0.706667
186 0XU 0.407407 0.828125
187 NB8 0.406593 0.688312
188 FYA 0.406593 0.736111
189 JB6 0.406593 0.697368
190 YSA 0.404255 0.630952
191 TYR AMP 0.404255 0.716216
192 ZDA 0.402439 0.742857
193 25L 0.402174 0.736111
194 4UV 0.4 0.706667
195 A A A 0.4 0.736111
196 101 0.4 0.708333
Ligand no: 2; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VSM; Ligand: 5AD; Similar sites found: 35
This union binding pocket(no: 1) in the query (biounit: 5vsm.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CC6 L5Y 0.02277 0.40016 1.88679
2 3RFA SAM 0.00000002084 0.64938 2.20126
3 3EXS 5RP 0.00666 0.42228 2.71493
4 2ZV2 609 0.0157 0.40415 3.02013
5 4UTU LRY 0.004185 0.42325 3.05677
6 4UTW RFW 0.001924 0.40892 3.05677
7 4FHD 0TT 0.000005179 0.55295 3.14465
8 4FHD EEM 0.000005179 0.55295 3.14465
9 5A89 ADP 0.02232 0.40044 3.20513
10 1Q6O LG6 0.001519 0.41399 3.24074
11 3HAV ATP 0.02718 0.40118 3.34448
12 3OVR 5SP 0.004363 0.41103 4.38596
13 5LY2 OGA 0.02284 0.40655 4.40252
14 1GET FAD 0.0483 0.40048 4.40252
15 4ZBY URA 0.02332 0.4141 4.63918
16 4U0O MTA 0.005434 0.40678 5.74324
17 3MI2 PFU 0.0243 0.40456 6.09319
18 2YN4 39J 0.01604 0.41478 6.77966
19 5TH5 MET 0.0000002836 0.65486 7.22433
20 5TH5 7C5 0.0007896 0.41611 7.22433
21 5EXK 5AD 0.0005556 0.40388 8.1761
22 1KTG AMP 0.02092 0.40368 8.69565
23 4NJH 2K8 0.00000004143 0.52324 9.13043
24 4NJH SAM 0.00000004143 0.52324 9.13043
25 4WVW SLT 0.008624 0.4237 10.4167
26 3C8F MT2 0.000005102 0.41219 11.4286
27 5A5W GUO 0.002675 0.44185 13.0435
28 1OLT SAM 0.0000016 0.5455 17.2956
29 3T7V SAM 0.0001844 0.46775 19.1824
30 4K38 SAM 0.00000000001652 0.77461 25.4717
31 4K37 SAM 0.00000000001244 0.72437 25.4717
32 4K39 SAM 0.00000000009169 0.70576 25.4717
33 2FB3 GTP 0.0000003163 0.60271 32.0755
34 2FB3 5AD 0.00000001228 0.60012 32.0755
35 2FB3 MET 0.00000002641 0.57438 32.0755
Pocket No.: 2; Query (leader) PDB : 5VSM; Ligand: MET; Similar sites found: 37
This union binding pocket(no: 2) in the query (biounit: 5vsm.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RFA SAM 0.00000002084 0.64938 2.20126
2 4AZT LY2 0.006521 0.42273 2.20126
3 2IHU TP9 0.01194 0.40797 2.20126
4 3EXS 5RP 0.006889 0.42157 2.71493
5 2ZV2 609 0.01535 0.40462 3.02013
6 4UTU LRY 0.003686 0.4258 3.05677
7 4UTW RFW 0.0015 0.41358 3.05677
8 4FHD EEM 0.000004023 0.55783 3.14465
9 4FHD 0TT 0.000004023 0.55783 3.14465
10 1Q6O LG6 0.001548 0.41304 3.24074
11 3OVR 5SP 0.004976 0.40858 4.38596
12 3B0X DGT 0.01007 0.41354 4.40252
13 5LY2 OGA 0.01978 0.40963 4.40252
14 2Q8C AKG 0.02118 0.40769 4.40252
15 5F7J ADE 0.01153 0.42189 4.71698
16 4U0O MTA 0.004004 0.41252 5.74324
17 2JBM SRT 0.009605 0.43236 6.35452
18 4R78 AMP 0.01821 0.40504 6.47249
19 2YN4 39J 0.01434 0.41713 6.77966
20 5TH5 MET 0.00000005934 0.68952 7.22433
21 5TH5 7C5 0.0009058 0.4137 7.22433
22 5EXK 5AD 0.0004129 0.41084 8.1761
23 1KTG AMP 0.02099 0.40353 8.69565
24 4NJH SAM 0.00000001987 0.53361 9.13043
25 4NJH 2K8 0.00000001987 0.53361 9.13043
26 3C8F MT2 0.000005102 0.41219 11.4286
27 5A5W GUO 0.003266 0.43788 13.0435
28 4BKS X6C 0.02673 0.40104 15.3846
29 1OLT SAM 0.0000007106 0.56044 17.2956
30 3T7V SAM 0.0001741 0.46882 19.1824
31 2ZRU FMN 0.01405 0.40581 20.7547
32 4K38 SAM 0.000000000006281 0.79275 25.4717
33 4K37 SAM 0.0000000000044 0.74294 25.4717
34 4K39 SAM 0.00000000003017 0.72569 25.4717
35 2FB3 GTP 0.0000003402 0.60131 32.0755
36 2FB3 5AD 0.00000001228 0.60012 32.0755
37 2FB3 MET 0.00000002641 0.57438 32.0755
Pocket No.: 3; Query (leader) PDB : 5VSM; Ligand: 5AD; Similar sites found: 2
This union binding pocket(no: 3) in the query (biounit: 5vsm.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2YPI PGA 0.0165 0.40309 4.8583
2 2ZRU FMN 0.01809 0.4008 20.7547
Pocket No.: 4; Query (leader) PDB : 5VSM; Ligand: MET; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 5vsm.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GET FAD 0.04769 0.40075 4.40252
2 2YPI PGA 0.01445 0.4059 4.8583
3 1VBR XYS XYP 0.01761 0.40577 10.0629
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