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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 1443 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 1205 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 1039 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: 203
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD 1 1
2 ADN 0.672727 0.854839
3 RAB 0.672727 0.854839
4 XYA 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 AOC 0.558824 0.828125
18 NEC 0.558824 0.885246
19 ZAS 0.552239 0.791045
20 A 0.552239 0.768116
21 AMP 0.552239 0.768116
22 LMS 0.552239 0.670886
23 ABM 0.550725 0.771429
24 A3N 0.550725 0.815385
25 6RE 0.544118 0.757143
26 SRA 0.544118 0.726027
27 3AM 0.537313 0.753623
28 DSH 0.536232 0.768116
29 MAO 0.535211 0.710526
30 3AD 0.532258 0.83871
31 SP1 0.529412 0.722222
32 RP1 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 A12 0.513889 0.716216
40 BA3 0.513889 0.746479
41 AP2 0.513889 0.716216
42 M33 0.513514 0.760563
43 AU1 0.513514 0.726027
44 MHZ 0.513514 0.710526
45 AP5 0.506849 0.746479
46 B4P 0.506849 0.746479
47 ADP 0.506849 0.746479
48 AN2 0.5 0.736111
49 A7D 0.5 0.80303
50 2AM 0.5 0.742857
51 SAM 0.5 0.75
52 PRX 0.5 0.75
53 AT4 0.5 0.716216
54 SA8 0.493506 0.771429
55 AD9 0.493506 0.726027
56 ADX 0.493333 0.670886
57 CA0 0.493333 0.726027
58 2BA 0.493151 0.764706
59 A3P 0.493151 0.742857
60 CMP 0.493151 0.776119
61 HEJ 0.486842 0.746479
62 50T 0.486842 0.736111
63 5X8 0.486842 0.815385
64 ACP 0.486842 0.726027
65 A3T 0.486842 0.857143
66 ATP 0.486842 0.746479
67 SFG 0.486842 0.828125
68 7D5 0.485294 0.684932
69 9ZA 0.481928 0.72
70 9ZD 0.481928 0.72
71 SMM 0.481481 0.72
72 ANP 0.481013 0.726027
73 5FA 0.480519 0.746479
74 APR 0.480519 0.746479
75 AR6 0.480519 0.746479
76 APC 0.480519 0.716216
77 AQP 0.480519 0.746479
78 A3S 0.48 0.815385
79 OVE 0.478873 0.712329
80 AAT 0.475 0.746479
81 5AL 0.475 0.760563
82 EEM 0.475 0.75
83 A5D 0.474359 0.815385
84 ADV 0.474359 0.716216
85 SAP 0.474359 0.706667
86 AGS 0.474359 0.706667
87 ADP PO3 0.474359 0.768116
88 RBY 0.474359 0.716216
89 QQX 0.471429 0.708333
90 5F1 0.469697 0.78125
91 A5A 0.469136 0.675
92 SAI 0.468354 0.779412
93 G5A 0.468354 0.630952
94 SAH 0.468354 0.791045
95 103 0.464789 0.764706
96 QQY 0.464789 0.71831
97 ACK 0.464789 0.761194
98 S7M 0.463415 0.75
99 ACQ 0.4625 0.726027
100 T99 0.4625 0.716216
101 GAP 0.4625 0.726027
102 TAT 0.4625 0.716216
103 3L1 0.461538 0.772727
104 3D1 0.461538 0.772727
105 54H 0.457831 0.658537
106 52H 0.457831 0.650602
107 VMS 0.457831 0.658537
108 PAP 0.455696 0.732394
109 A2P 0.453333 0.753623
110 NOC 0.453125 0.790323
111 5I5 0.453125 0.913793
112 53H 0.452381 0.650602
113 DAL AMP 0.452381 0.760563
114 MAP 0.452381 0.706667
115 TSB 0.452381 0.666667
116 ADP ALF 0.451219 0.706667
117 ATF 0.451219 0.716216
118 ALF ADP 0.451219 0.706667
119 2VA 0.448718 0.830769
120 8QN 0.447059 0.760563
121 5SV 0.447059 0.710526
122 6YZ 0.445783 0.726027
123 SRP 0.445783 0.716216
124 VO4 ADP 0.445783 0.736111
125 SSA 0.445783 0.630952
126 ADP VO4 0.445783 0.736111
127 LSS 0.44186 0.635294
128 0UM 0.44186 0.760563
129 PAJ 0.44186 0.701299
130 7D3 0.44 0.666667
131 PPS 0.439024 0.65
132 1ZZ 0.438202 0.683544
133 NVA 2AD 0.4375 0.782609
134 62X 0.436782 0.72
135 NVA LMS 0.436782 0.627907
136 A22 0.435294 0.736111
137 D3Y 0.435294 0.791045
138 8X1 0.435294 0.609195
139 5CA 0.435294 0.630952
140 KB1 0.433333 0.736111
141 MYR AMP 0.433333 0.683544
142 ARJ 0.432836 0.774194
143 VRT 0.432099 0.794118
144 SO8 0.432099 0.818182
145 9X8 0.431818 0.72973
146 LEU LMS 0.431818 0.627907
147 K15 0.431818 0.739726
148 OAD 0.431818 0.75
149 S8M 0.430233 0.757143
150 OOB 0.430233 0.736111
151 GEK 0.430233 0.757143
152 25A 0.430233 0.746479
153 WAQ 0.426966 0.697368
154 GSU 0.426966 0.630952
155 3NZ 0.426966 0.782609
156 ADZ 0.425926 0.618182
157 AMO 0.425287 0.716216
158 ADQ 0.425287 0.726027
159 A1R 0.425287 0.697368
160 NSS 0.425287 0.630952
161 DSZ 0.425287 0.630952
162 A3R 0.425287 0.697368
163 4AD 0.425287 0.706667
164 2A5 0.425 0.68
165 TXA 0.422222 0.739726
166 BIS 0.422222 0.697368
167 9K8 0.422222 0.627907
168 3OD 0.422222 0.75
169 ME8 0.422222 0.683544
170 PTJ 0.422222 0.710526
171 SXZ 0.422222 0.75
172 00A 0.420455 0.697368
173 DLL 0.420455 0.736111
174 AHX 0.420455 0.688312
175 ATR 0.419753 0.742857
176 7D4 0.417722 0.666667
177 TAD 0.416667 0.679487
178 ADP BMA 0.41573 0.726027
179 3UK 0.41573 0.726027
180 A6D 0.41573 0.716216
181 26A 0.411765 0.787879
182 AFX 0.411765 0.716418
183 LAD 0.411111 0.679487
184 KAA 0.411111 0.609195
185 PR8 0.411111 0.670886
186 B5V 0.411111 0.716216
187 P5A 0.411111 0.602273
188 A A 0.411111 0.746479
189 V3L 0.409639 0.746479
190 B5M 0.408602 0.72973
191 YAP 0.408602 0.706667
192 B5Y 0.408602 0.72973
193 0XU 0.407407 0.828125
194 FYA 0.406593 0.736111
195 JB6 0.406593 0.697368
196 NB8 0.406593 0.688312
197 YSA 0.404255 0.630952
198 ZDA 0.402439 0.742857
199 25L 0.402174 0.736111
200 A A A 0.4 0.736111
201 101 0.4 0.708333
202 4UV 0.4 0.706667
203 TYR AMP 0.4 0.706667
Ligand no: 2; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MED 1 1
2 MET 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 MF3 0.5 0.647059
7 NVA 0.5 0.758621
8 HSE 0.466667 0.617647
9 DAB 0.466667 0.636364
10 MHO 0.457143 0.717949
11 SME 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 DGL 0.424242 0.625
22 GGL 0.424242 0.625
23 GLU 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 FME 0.410256 0.84375
27 AME 0.410256 0.771429
28 LEU 0.40625 0.666667
29 JM6 0.4 0.7
30 CYS 0.4 0.666667
31 DCY 0.4 0.666667
32 C2N 0.4 0.633333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VSM; Ligand: 5AD; Similar sites found with APoc: 87
This union binding pocket(no: 1) in the query (biounit: 5vsm.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1L5Y BEF None
2 1FHW I5P None
3 1MFI FHC None
4 4CC6 L5Y 1.88679
5 1Y9Q MED 2.08333
6 3RFA SAM 2.20126
7 3N9R TD3 2.28013
8 5G4L NDP 2.44755
9 3VPD ANP 2.4911
10 3U6W KIV 2.51572
11 2GDZ NAD 2.62172
12 3EXS 5RP 2.71493
13 2ZV2 609 3.02013
14 4UTU LRY 3.05677
15 4UTW RFW 3.05677
16 4FHD EEM 3.14465
17 4FHD 0TT 3.14465
18 2FLI DX5 3.18182
19 5A89 ADP 3.20513
20 1Q6O LG6 3.24074
21 3HAV ATP 3.34448
22 2F6U CIT 3.4188
23 2FJK 13P 3.60656
24 2QK4 ATP 3.77358
25 4P4M D3T 3.77358
26 5YSI NCA 3.94737
27 5E62 Z3Q GAL 5N6 4.02685
28 4JYD SAH 4.08805
29 2ZUX RAM 4.08805
30 6BXL SAM 4.08805
31 1M0W ANP 4.08805
32 1CX9 NHP 4.10448
33 3OVR 5SP 4.38596
34 5LY1 PPI 4.40252
35 5LY2 OGA 4.40252
36 3VZS NAP 4.40252
37 1Q8Y ADE 4.40252
38 5USZ SKE 4.49827
39 2BS3 CIT 4.60251
40 1NJJ GET 4.71698
41 3B8I OXL 4.87805
42 2Y88 2ER 4.91803
43 2XK9 XK9 4.96894
44 1RJW ETF 5.03145
45 2GQR ADP 5.06329
46 2BMB PMM 5.34591
47 4XZ3 ACP 5.34591
48 6ACS CIT 5.42636
49 4NFE BEN 5.48523
50 4U0O MTA 5.74324
51 5ZCT ANP 5.88235
52 3MI2 PFU 6.09319
53 2F2T 5IQ 6.21118
54 2F62 12M 6.21118
55 4NBT NAD 6.25
56 5G48 1FL 6.60377
57 2YN4 39J 6.77966
58 3H22 B53 7.07071
59 5TH5 MET 7.22433
60 5TH5 7C5 7.22433
61 4C2C ALA ALA ALA 7.2327
62 4S00 AKR 7.2327
63 2D3Y DU 7.76256
64 5EXK 5AD 8.1761
65 5EXK MET 8.1761
66 1DQX BMP 8.2397
67 1KTG AMP 8.69565
68 1GYM MYG 8.72483
69 1M3U KPL 9.09091
70 4NJH SAM 9.13043
71 4NJH 2K8 9.13043
72 5F90 LMR 10.2564
73 5F90 GLA GAL 10.2564
74 4WVW SLT 10.4167
75 3C8F MT2 11.4286
76 1VKF CIT 12.234
77 5A5W GUO 13.0435
78 5T9C G3P 13.0597
79 5CLO NS8 16.9492
80 1OLT SAM 17.2956
81 3T7V SAM 19.1824
82 4K38 SAM 25.4717
83 4K37 SAM 25.4717
84 4K39 SAM 25.4717
85 2FB3 GTP 32.0755
86 2FB3 5AD 32.0755
87 2FB3 MET 32.0755
Pocket No.: 2; Query (leader) PDB : 5VSM; Ligand: MET; Similar sites found with APoc: 105
This union binding pocket(no: 2) in the query (biounit: 5vsm.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1FHW I5P None
2 1L5Y BEF None
3 1MFI FHC None
4 4I6H 1C8 1.94805
5 1GU3 BGC BGC BGC BGC BGC 2.01342
6 5GVR LMR 2.13675
7 3RFA SAM 2.20126
8 2IHU TP9 2.20126
9 3N9R TD3 2.28013
10 5G4L NDP 2.44755
11 3VPD ANP 2.4911
12 3VPD BUA 2.4911
13 3DLS ADP 2.51572
14 4E70 N7I 2.51572
15 3U6W KIV 2.51572
16 2GDZ NAD 2.62172
17 3EXS 5RP 2.71493
18 2ZV2 609 3.02013
19 4UTU LRY 3.05677
20 4UTW RFW 3.05677
21 4FHD 0TT 3.14465
22 4FHD EEM 3.14465
23 2YNE YNE 3.14465
24 2YNE NHW 3.14465
25 5C03 AGS 3.14465
26 2FLI DX5 3.18182
27 1Q6O LG6 3.24074
28 2F6U CIT 3.4188
29 2FJK 13P 3.60656
30 5WBF LAC 3.7037
31 3HQP FDP 3.77358
32 2QK4 ATP 3.77358
33 5YSI NCA 3.94737
34 2ZUX RAM 4.08805
35 4JYD SAH 4.08805
36 6BXL SAM 4.08805
37 1M0W ANP 4.08805
38 3K5I ADP 4.08805
39 1CX9 NHP 4.10448
40 3OVR 5SP 4.38596
41 5LY1 PPI 4.40252
42 5ZIC BMA Z4Y NAG 4.40252
43 3B0X DGT 4.40252
44 5LY2 OGA 4.40252
45 5FWE OGA 4.40252
46 1Q8Y ADE 4.40252
47 3VZS NAP 4.40252
48 5F7J ADE 4.71698
49 1NJJ GET 4.71698
50 4QYS PLP SEP 4.71698
51 5X8I SQZ 4.71698
52 3G4Q MCH 4.79452
53 3B8I OXL 4.87805
54 2Y88 2ER 4.91803
55 3A06 NDP 5.03145
56 1RJW ETF 5.03145
57 2GQR ADP 5.06329
58 2BMB PMM 5.34591
59 4XZ3 ACP 5.34591
60 6ACS CIT 5.42636
61 4NFE BEN 5.48523
62 4U0O MTA 5.74324
63 5ZCT ANP 5.88235
64 2F2T 5IQ 6.21118
65 2F62 12M 6.21118
66 2F67 12B 6.21118
67 4NBT NAD 6.25
68 2JBM SRT 6.35452
69 4R78 AMP 6.47249
70 5G48 1FL 6.60377
71 2YN4 39J 6.77966
72 1QFT HSM 6.85714
73 3H22 B53 7.07071
74 5TH5 MET 7.22433
75 5TH5 7C5 7.22433
76 4C2C ALA ALA ALA 7.2327
77 5TCI MLI 7.54717
78 2BKK ADP 7.69231
79 2D3Y DU 7.76256
80 2ET1 GLV 7.9602
81 5EXK 5AD 8.1761
82 5EXK MET 8.1761
83 1XMY ROL 8.1761
84 1KTG AMP 8.69565
85 4NJH SAM 9.13043
86 4NJH 2K8 9.13043
87 4I5I 4I5 10.1045
88 3QLM PLM 11.2903
89 3C8F MT2 11.4286
90 1VKF CIT 12.234
91 5A5W GUO 13.0435
92 5T9C G3P 13.0597
93 4BKS X6C 15.3846
94 1T36 ORN 15.7233
95 5CLO NS8 16.9492
96 1OLT SAM 17.2956
97 3T7V SAM 19.1824
98 2ZRU FMN 20.7547
99 4C2W ANP 25
100 4K38 SAM 25.4717
101 4K37 SAM 25.4717
102 4K39 SAM 25.4717
103 2FB3 GTP 32.0755
104 2FB3 5AD 32.0755
105 2FB3 MET 32.0755
Pocket No.: 3; Query (leader) PDB : 5VSM; Ligand: 5AD; Similar sites found with APoc: 12
This union binding pocket(no: 3) in the query (biounit: 5vsm.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1SR9 KIV 2.51572
2 5B4T 3HR 2.69231
3 5B4T NAD 2.69231
4 1PIG BGC 3.14465
5 5AE2 FAD 3.45912
6 3VZS CAA 4.40252
7 1GET FAD 4.40252
8 5FWE OGA 4.40252
9 2YPI PGA 4.8583
10 4HKP TKW 8.65385
11 5X2N ALA 13.8249
12 2ZRU FMN 20.7547
Pocket No.: 4; Query (leader) PDB : 5VSM; Ligand: MET; Similar sites found with APoc: 17
This union binding pocket(no: 4) in the query (biounit: 5vsm.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1SR9 KIV 2.51572
2 3ZGJ RMN 2.51572
3 5B4T NAD 2.69231
4 5B4T 3HR 2.69231
5 1PIG BGC 3.14465
6 5AE2 FYC 3.45912
7 4P4M D3T 3.77358
8 5ZYN FMN 3.77358
9 2YYE APC 4.08805
10 5X9D 80F 4.27632
11 1GET FAD 4.40252
12 2YPI PGA 4.8583
13 4W6Z ETF 6.60377
14 4S00 AKR 7.2327
15 1VBR XYS XYP 10.0629
16 5F90 LMR 10.2564
17 5Y4R C2E 10.3448
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