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Receptor
PDB id Resolution Class Description Source Keywords
3PA1 1.48 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF P DOMAIN FROM NORWALK VIRUS STRAIN VIET COMPLEX WITH HBGA TYPE A NORWALK VIRUS NOROVIRUS P-DOMAIN CAPSID RECEPTOR HISTO BLOOD GROUP ANT(HBGA) VIRAL PROTEIN
Ref.: CRYSTAL STRUCTURES OF GII.10 AND GII.12 NOROVIRUS P DOMAINS IN COMPLEX WITH HISTO-BLOOD GROUP ANTIGENS DETAILS FOR A POTENTIAL SITE OF VULNERABILITY. J.VIROL. V. 85 6687 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:10;
A:13;
A:15;
A:16;
A:5;
A:6;
A:7;
A:8;
B:1;
B:11;
B:12;
B:14;
B:2;
B:4;
B:9;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
FUC GAL A2G A:1;
Valid;
none;
submit data
529.492 n/a O=C(N...
IMD A:18;
B:17;
Invalid;
Invalid;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6GW1 1.9 Å NON-ENZYME: OTHER GII.10 HUMAN NOROVIRUS PROTRUDING DOMAIN IN COMPLEX WITH GLYCOCHENODEOXYCHOLATE (GCDCA) NORWALK VIRUS NOROVIRUS GII.10 P DOMAIN GCDCA HBGA VIRAL PROTEIN
Ref.: STRUCTURAL BASIS FOR HUMAN NOROVIRUS CAPSID BINDING ACIDS. J. VIROL. 2018
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4Z4W - FUL C6 H12 O5 C[C@H]1[C@....
2 6GW1 Kd = 0.00000145 M CHO C26 H43 N O5 C[C@H](CCC....
3 4Z4Z - FUC GLA GLA n/a n/a
4 3ONY - FUC C6 H12 O5 C[C@H]1[C@....
5 3Q3A - FUL GAL NAG n/a n/a
6 4Z4T - FUL C6 H12 O5 C[C@H]1[C@....
7 4Z4V - FUL C6 H12 O5 C[C@H]1[C@....
8 4Z4Y - FUC GLA GLA n/a n/a
9 5BSY - FLC C6 H5 O7 C(C(=O)[O-....
10 5HZB ic50 = 5.5 mM GLC GAL FUC n/a n/a
11 3PA2 - FUC GAL NAG FUC n/a n/a
12 4Z4S - FUL C6 H12 O5 C[C@H]1[C@....
13 3Q38 - FUC GAL GLA n/a n/a
14 3RY8 Kd = 460 uM FLC C6 H5 O7 C(C(=O)[O-....
15 3PA1 - FUC GAL A2G n/a n/a
16 6GW2 Kd = 0.0000123 M TUD C26 H45 N O6 S C[C@H](CCC....
17 4Z4U - FUL C6 H12 O5 C[C@H]1[C@....
18 3Q39 - FUC GAL n/a n/a
19 5HZA ic50 = 5.6 mM FUC BGC GAL n/a n/a
20 5BSX - FLC C6 H5 O7 C(C(=O)[O-....
21 6GY9 - KBA C10 H17 N3 O5 C[C@H]1[C@....
22 4Z4R - FUL C6 H12 O5 C[C@H]1[C@....
70% Homology Family (44)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4OPS - FUC GAL NAG FUC n/a n/a
2 4OPO - FUC NAG GAL FUC n/a n/a
3 4WZL - FUC NDG GAL n/a n/a
4 4X06 - FUC GLA GLA n/a n/a
5 4WZE - FUC NDG GAL FUC n/a n/a
6 4OP7 - FUC GLA GLA n/a n/a
7 4X05 - FUC GLA GLA n/a n/a
8 4WZT - FUC GLA A2G n/a n/a
9 4X0C - FUC NDG GAL n/a n/a
10 4WZK - FUC GAL NDG n/a n/a
11 4X07 - FUC GLA A2G n/a n/a
12 5LKC ic50 = 13 mM FUC GLA A2G n/a n/a
13 5LKG - FUC GAL GLC n/a n/a
14 6GW0 Kd = 0.00000145 M TUD C26 H45 N O6 S C[C@H](CCC....
15 6GVZ Kd = 0.4 uM CHO C26 H43 N O5 C[C@H](CCC....
16 4Z4W - FUL C6 H12 O5 C[C@H]1[C@....
17 6GW1 Kd = 0.00000145 M CHO C26 H43 N O5 C[C@H](CCC....
18 4Z4Z - FUC GLA GLA n/a n/a
19 3ONY - FUC C6 H12 O5 C[C@H]1[C@....
20 3Q3A - FUL GAL NAG n/a n/a
21 4Z4T - FUL C6 H12 O5 C[C@H]1[C@....
22 4Z4V - FUL C6 H12 O5 C[C@H]1[C@....
23 4Z4Y - FUC GLA GLA n/a n/a
24 5BSY - FLC C6 H5 O7 C(C(=O)[O-....
25 5HZB ic50 = 5.5 mM GLC GAL FUC n/a n/a
26 3PA2 - FUC GAL NAG FUC n/a n/a
27 4Z4S - FUL C6 H12 O5 C[C@H]1[C@....
28 3Q38 - FUC GAL GLA n/a n/a
29 3RY8 Kd = 460 uM FLC C6 H5 O7 C(C(=O)[O-....
30 3PA1 - FUC GAL A2G n/a n/a
31 6GW2 Kd = 0.0000123 M TUD C26 H45 N O6 S C[C@H](CCC....
32 4Z4U - FUL C6 H12 O5 C[C@H]1[C@....
33 3Q39 - FUC GAL n/a n/a
34 5HZA ic50 = 5.6 mM FUC BGC GAL n/a n/a
35 5BSX - FLC C6 H5 O7 C(C(=O)[O-....
36 6GY9 - KBA C10 H17 N3 O5 C[C@H]1[C@....
37 4Z4R - FUL C6 H12 O5 C[C@H]1[C@....
38 4RM0 - FUC NAG GAL n/a n/a
39 3PUN - FUC GAL NDG FUC n/a n/a
40 3PVD - SIA GAL NDG FUC n/a n/a
41 3R6K - FUC GAL GLA n/a n/a
42 6GW4 Kd = 0.00000145 M CHO C26 H43 N O5 C[C@H](CCC....
43 2OBS - FUC GL0 A2G n/a n/a
44 2OBT - FUC GAL GLA n/a n/a
50% Homology Family (55)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 4OPS - FUC GAL NAG FUC n/a n/a
2 4OPO - FUC NAG GAL FUC n/a n/a
3 4WZL - FUC NDG GAL n/a n/a
4 4X06 - FUC GLA GLA n/a n/a
5 4WZE - FUC NDG GAL FUC n/a n/a
6 4OP7 - FUC GLA GLA n/a n/a
7 4X05 - FUC GLA GLA n/a n/a
8 4WZT - FUC GLA A2G n/a n/a
9 4X0C - FUC NDG GAL n/a n/a
10 4WZK - FUC GAL NDG n/a n/a
11 4X07 - FUC GLA A2G n/a n/a
12 5LKC ic50 = 13 mM FUC GLA A2G n/a n/a
13 5LKG - FUC GAL GLC n/a n/a
14 6GW0 Kd = 0.00000145 M TUD C26 H45 N O6 S C[C@H](CCC....
15 6GVZ Kd = 0.4 uM CHO C26 H43 N O5 C[C@H](CCC....
16 4Z4W - FUL C6 H12 O5 C[C@H]1[C@....
17 6GW1 Kd = 0.00000145 M CHO C26 H43 N O5 C[C@H](CCC....
18 4Z4Z - FUC GLA GLA n/a n/a
19 3ONY - FUC C6 H12 O5 C[C@H]1[C@....
20 3Q3A - FUL GAL NAG n/a n/a
21 4Z4T - FUL C6 H12 O5 C[C@H]1[C@....
22 4Z4V - FUL C6 H12 O5 C[C@H]1[C@....
23 4Z4Y - FUC GLA GLA n/a n/a
24 5BSY - FLC C6 H5 O7 C(C(=O)[O-....
25 5HZB ic50 = 5.5 mM GLC GAL FUC n/a n/a
26 3PA2 - FUC GAL NAG FUC n/a n/a
27 4Z4S - FUL C6 H12 O5 C[C@H]1[C@....
28 3Q38 - FUC GAL GLA n/a n/a
29 3RY8 Kd = 460 uM FLC C6 H5 O7 C(C(=O)[O-....
30 3PA1 - FUC GAL A2G n/a n/a
31 6GW2 Kd = 0.0000123 M TUD C26 H45 N O6 S C[C@H](CCC....
32 4Z4U - FUL C6 H12 O5 C[C@H]1[C@....
33 3Q39 - FUC GAL n/a n/a
34 5HZA ic50 = 5.6 mM FUC BGC GAL n/a n/a
35 5BSX - FLC C6 H5 O7 C(C(=O)[O-....
36 6GY9 - KBA C10 H17 N3 O5 C[C@H]1[C@....
37 4Z4R - FUL C6 H12 O5 C[C@H]1[C@....
38 4RM0 - FUC NAG GAL n/a n/a
39 3PUN - FUC GAL NDG FUC n/a n/a
40 3PVD - SIA GAL NDG FUC n/a n/a
41 4RDL - FUC GAL NDG FUC n/a n/a
42 4RDK - FUC NDG GAL FUC n/a n/a
43 3R6K - FUC GAL GLA n/a n/a
44 5N7M - GLC GAL FUC n/a n/a
45 2ZL6 - FUC GAL NAG GAL BGC n/a n/a
46 2ZL7 - FUC GAL NGA n/a n/a
47 3D26 - NGA GAL FUC n/a n/a
48 4P25 - FUC GAL NAG FUC n/a n/a
49 4P3I - GAL NAG FUC n/a n/a
50 4P2N - GAL NAG FUC n/a n/a
51 4P26 - A2G GAL NAG FUC n/a n/a
52 4P1V - FUC GAL NAG n/a n/a
53 6GW4 Kd = 0.00000145 M CHO C26 H43 N O5 C[C@H](CCC....
54 2OBS - FUC GL0 A2G n/a n/a
55 2OBT - FUC GAL GLA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FUC GAL A2G; Similar ligands found: 176
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA GAL FUC 1 1
2 FUC GLA A2G 1 1
3 A2G GAL FUC 1 1
4 A2G GLA FUC 1 1
5 FUC GAL A2G 1 1
6 GAL GAL FUC 0.691176 0.73913
7 FUC GAL GLA 0.691176 0.73913
8 GLA GAL FUC 0.691176 0.73913
9 FUC GLA GLA 0.691176 0.73913
10 GLA GLA FUC 0.691176 0.73913
11 BGC FUC GAL FUC A2G 0.682927 0.978723
12 GLC FUC GAL FUC A2G 0.682927 0.978723
13 FUC GAL NAG A2G 0.674699 0.938776
14 A2G GAL BGC FUC 0.674699 1
15 A2G GAL NAG FUC 0.674699 0.938776
16 NAG GAL FUC FUC A2G 0.658824 0.938776
17 FUC GAL NAG A2G FUC 0.658824 0.938776
18 FUC BGC GAL NAG 0.650602 1
19 BGA 0.627907 0.836364
20 GAL NAG 0.597222 0.978261
21 NAG GAL 0.597222 0.978261
22 NAG A2G 0.589041 0.958333
23 NAG NGA 0.589041 0.958333
24 A2G GAL NAG FUC GAL GLC 0.583333 0.938776
25 GLC GAL NAG GAL FUC A2G 0.583333 0.938776
26 FUC GAL NGA 0.580247 0.918367
27 GAL NGA A2G 0.564103 0.958333
28 DR3 0.555556 1
29 NAG MAN BMA 0.55 0.978261
30 NAG GDL 0.546667 0.958333
31 CBS 0.546667 0.958333
32 NAG MBG 0.546667 0.978723
33 NDG NAG 0.546667 0.958333
34 CBS CBS 0.546667 0.958333
35 NGA GAL BGC 0.5375 0.978261
36 NAG FUC 0.533333 0.956522
37 NGA GAL 0.532468 0.916667
38 FUC NDG GAL 0.530864 1
39 GAL NDG FUC 0.530864 1
40 GAL NAG GAL FUC 0.528736 1
41 GLA NAG GAL FUC 0.528736 1
42 FUC GAL 0.528571 0.717391
43 FUC NAG 0.525641 0.9
44 NAG GAL FUC 0.52439 1
45 DR2 0.52439 1
46 FUC GAL NDG 0.52439 1
47 FUC GAL NAG 0.52439 1
48 GAL NAG FUC 0.52439 1
49 FUL GAL NAG 0.52439 1
50 NDG GAL FUC 0.52439 1
51 FUC BGC GAL NAG GAL 0.521277 1
52 MBG A2G 0.519481 0.978723
53 A2G MBG 0.519481 0.978723
54 NAG NAG NAG NAG NDG 0.518987 0.938776
55 NAG NAG NAG NAG NAG NAG NAG NAG 0.518987 0.938776
56 NDG NAG NAG NAG 0.518987 0.938776
57 NAG NAG NAG NAG NAG NAG 0.518987 0.938776
58 NAG NAG NAG NAG NAG 0.518987 0.938776
59 NAG NAG NDG NAG 0.518987 0.938776
60 NDG NAG NAG NDG 0.518987 0.938776
61 NAG NAG NDG 0.518987 0.938776
62 CTO 0.518987 0.938776
63 NAG NAG NAG NDG 0.518987 0.938776
64 NDG NAG NAG 0.518987 0.938776
65 NAG GAL NAG 0.511905 0.958333
66 NAG GAL BGC 0.511905 0.978261
67 GLA MAN ABE 0.506173 0.708333
68 NAG MAN MMA 0.506024 0.978723
69 FUC NAG GAL FUC 0.505882 0.978723
70 GAL NDG FUC FUC 0.505882 0.978723
71 BCW 0.505882 0.978723
72 FUC GAL NAG FUC 0.505882 0.978723
73 FUC GAL NDG FUC 0.505882 0.978723
74 GAL NAG FUC FUC 0.505882 0.978723
75 FUC NDG GAL FUC 0.505882 0.978723
76 BDZ 0.505882 0.978723
77 FUC GAL NAG GAL FUC 0.505495 0.978723
78 NGA GLA GAL BGC 0.5 0.978261
79 NAG BDP NAG BDP NAG BDP NAG 0.5 0.92
80 NAG NAG 0.5 0.865385
81 3QL 0.5 0.884615
82 FUC NAG GAL 0.5 0.92
83 NAG NDG 0.5 0.865385
84 MAN MAN NAG 0.494118 0.9375
85 MAG FUC GAL 0.493976 0.958333
86 NAG MAN MAN 0.488372 0.978261
87 FUC BGC GAL 0.487179 0.73913
88 GLA GAL NAG FUC GAL GLC 0.484848 1
89 NAG MAN MAN MAN NAG 0.483516 0.958333
90 FUC GAL NAG GAL BGC 0.479167 1
91 GLC NAG GAL GAL FUC 0.479167 1
92 GAL GLC NAG GAL FUC 0.479167 1
93 GAL NAG MAN 0.47619 0.978261
94 NAG MAN 0.475 0.9375
95 MAG 0.471429 0.914894
96 2F8 0.471429 0.914894
97 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.469388 0.92
98 GAL A2G 0.467532 0.978261
99 GAL NGA 0.467532 0.978261
100 A2G GAL 0.467532 0.978261
101 NAG A2G GAL 0.465909 0.958333
102 NAG MUB 0.465909 0.92
103 AH0 NAG 0.465909 0.851852
104 NAG AMU 0.465909 0.92
105 NAG NAG NAG 0.45977 0.867925
106 NAG NAG NAG NAG 0.45977 0.867925
107 FUC NAG GLA GAL 0.457447 0.978723
108 BMA Z4Y NAG 0.456522 0.957447
109 Z4S NAG NAG 0.455556 0.867925
110 NAG MAN BMA MAN NAG GAL 0.45098 0.958333
111 BGC GLA GAL FUC 0.448276 0.73913
112 NG1 0.445946 0.736842
113 GN1 0.445946 0.736842
114 GLC GAL NAG GAL FUC FUC 0.445545 0.978723
115 BGC GAL NAG GAL FUC FUC 0.445545 0.978723
116 NAG GAL GAL NAG GAL 0.444444 0.958333
117 NAG NM9 0.443182 0.901961
118 LEC NGA 0.44086 0.71875
119 LAT FUC 0.439024 0.73913
120 GLC GAL FUC 0.439024 0.73913
121 8B7 0.439024 0.73913
122 BGC GAL FUC 0.439024 0.73913
123 FUC GAL GLC 0.439024 0.73913
124 NGT NAG 0.438202 0.793103
125 3PV 0.4375 0.92
126 FUC NAG TA5 0.431579 0.671642
127 NLC 0.43038 0.978261
128 NDG GAL 0.43038 0.978261
129 GAL NDG 0.43038 0.978261
130 GAL MGC 0.43038 0.978723
131 FUC C4W NAG BMA 0.43 0.884615
132 GAL NAG GAL NAG GAL NAG 0.428571 0.938776
133 NAG GAL GAL NAG 0.428571 0.958333
134 DLD 0.428571 0.793103
135 FUC C4W NAG BMA MAN NAG 0.428571 0.884615
136 MMA MAN NAG MAN NAG NAG 0.427083 0.92
137 NAG AH0 0.425532 0.851852
138 NOJ NAG NAG NAG 0.423913 0.821429
139 GLC GAL NAG GAL 0.423913 0.978261
140 LAT NAG GAL 0.423913 0.978261
141 NOJ NAG NAG 0.423913 0.836364
142 GAL NAG GAL 0.422222 0.9375
143 WZ5 0.42 0.978723
144 GYU 0.419753 0.785714
145 TNR 0.419753 0.843137
146 3YW 0.417722 0.893617
147 BGC GAL NAG GAL 0.417582 0.978261
148 GAL NAG GAL GLC 0.417582 0.978261
149 SGA MAG FUC 0.416667 0.692308
150 FUC C4W NAG BMA MAN MAN NAG NAG 0.415254 0.884615
151 NAG BMA NAG MAN MAN NAG NAG 0.415094 0.938776
152 NAG MAN BMA NDG MAN NAG GAL 0.412844 0.938776
153 FHY 0.412371 0.867925
154 GAL NAG GAL BGC 0.410526 0.9375
155 NAG NAG NGT 0.410526 0.779661
156 6Y2 0.410526 0.71875
157 SN5 SN5 0.409639 0.823529
158 M5G 0.409091 0.958333
159 NAG NAG BMA MAN MAN NAG GAL NAG 0.409091 0.938776
160 FUC C4W NAG BMA MAN MAN NAG 0.408333 0.884615
161 FUC C4W NAG BMA MAN 0.407407 0.884615
162 BGB 0.406593 0.648148
163 G4S MAG FUC 0.40625 0.692308
164 MA8 0.404762 0.826923
165 XYS GAL FUC 0.402299 0.723404
166 MAN BMA NAG 0.402299 0.978261
167 GLA GAL NAG 0.402299 0.978261
168 NAG NAG BMA 0.402174 0.884615
169 NAG NDG BMA 0.402174 0.884615
170 NDG 0.4 0.869565
171 GAL NGA GLA BGC GAL 0.4 0.978261
172 A2G 0.4 0.869565
173 BM3 0.4 0.869565
174 NGA 0.4 0.869565
175 HSQ 0.4 0.869565
176 NAG 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6GW1; Ligand: CHO; Similar sites found with APoc: 39
This union binding pocket(no: 1) in the query (biounit: 6gw1.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4RF7 ARG 2.2293
2 3JU6 ANP 2.2293
3 2J5B TYE 2.2293
4 6FBA D48 2.2293
5 3E7S AT2 2.54777
6 4WOE ADP 2.54777
7 5H9Y BGC BGC BGC BGC BGC 2.54777
8 1H8S AIC 2.77778
9 4YVN EBS 2.86624
10 2PNC CLU 2.86624
11 5MJA 7O3 2.95082
12 3KJQ B94 3.15789
13 2Z3U CRR 3.50318
14 5M6N 7H9 4.23729
15 3UW5 MAA CHG PRO 0DQ 4.31034
16 4MTI 2DX 4.34783
17 1Z03 OCH 4.4586
18 1VJ7 GDP 4.77707
19 4B1L FRU 4.84848
20 1U25 IHS 5.09554
21 1GU3 BGC BGC BGC BGC BGC 6.04027
22 1MJT ITU 6.05096
23 4CM9 YGL 6.25
24 5GLT BGC GAL NAG GAL 6.33803
25 6CAY ERG 7.10059
26 2E27 AB0 7.93651
27 2BOS GLA GAL GLC 8.82353
28 2BOS GLA GAL 8.82353
29 3M3E GAL A2G NPO 9.31677
30 2I74 MAN MAN MAN MAN 10.0529
31 3HCH RSM 10.274
32 6GNO XDI 11.1111
33 5OCG 9R5 11.6402
34 4WVW SLT 11.8056
35 3CM2 X23 12.3077
36 5ZMY TAR 12.7389
37 3WG3 A2G GAL NAG FUC 15.1685
38 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 15.7895
39 3IWD M2T 27.4194
Pocket No.: 2; Query (leader) PDB : 6GW1; Ligand: CHO; Similar sites found with APoc: 11
This union binding pocket(no: 2) in the query (biounit: 6gw1.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 6MPT C30 2.7972
2 2VL1 GLY GLY 3.18471
3 2F2H XTG 3.82166
4 1I82 BGC BGC 4.2328
5 1VKF CIT 5.73248
6 4Y8D 49J 6.42857
7 1WW5 SGA BGC 9.375
8 4F8L AES 9.65517
9 3ZXE PGZ 9.77444
10 1LSH PLD 9.87261
11 4YLZ LAT NAG GAL 10.4575
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