Receptor
PDB id Resolution Class Description Source Keywords
4P2N 1.7 Å NON-ENZYME: OTHER STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN C WITH LEX HBGA NOROVIRUS HU/GI.7/TCH-060/USA/2003 P DOMAIN CAPSID PROTEIN NOROVIRUS HBGA LEY LEWIS HBGA NONSECRETOR VIRAL PROTEIN
Ref.: STRUCTURAL ANALYSIS OF DETERMINANTS OF HISTO-BLOOD ANTIGEN BINDING SPECIFICITY IN GENOGROUP I NOROVIRU J.VIROL. V. 88 6168 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG FUC GAL H:1;
G:1;
F:1;
E:1;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
529.492 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P25 1.5 Å NON-ENZYME: OTHER STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN C WITH LEY HBGA. NOROVIRUS HU/GI.7/TCH-060/USA/2003 P DOMAIN CAPSID PROTEIN NOROVIRUS HBGA LEY LEWIS HBGA PROTEIN
Ref.: STRUCTURAL ANALYSIS OF DETERMINANTS OF HISTO-BLOOD ANTIGEN BINDING SPECIFICITY IN GENOGROUP I NOROVIRU J.VIROL. V. 88 6168 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4P25 - NAG FUC GAL FUC n/a n/a
2 4P3I - NAG GAL FUC n/a n/a
3 4P2N - NAG FUC GAL n/a n/a
4 4P26 - NAG GAL FUC A2G n/a n/a
5 4P1V - NAG GAL FUC n/a n/a
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4RDL - NDG FUC GAL FUC n/a n/a
2 4RDK - NDG GAL FUC FUC n/a n/a
3 5N7M - GLC GAL FUC n/a n/a
4 2ZL6 - BGC GAL NAG GAL FUC n/a n/a
5 2ZL7 - GAL FUC NGA n/a n/a
6 3D26 - GAL FUC NGA n/a n/a
7 4P25 - NAG FUC GAL FUC n/a n/a
8 4P3I - NAG GAL FUC n/a n/a
9 4P2N - NAG FUC GAL n/a n/a
10 4P26 - NAG GAL FUC A2G n/a n/a
11 4P1V - NAG GAL FUC n/a n/a
50% Homology Family (59)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4OPS - NAG GAL FUC FUC n/a n/a
2 4OPO - NAG GAL FUC FUC n/a n/a
3 4WZL - NDG GAL FUC n/a n/a
4 4X06 - GLA FUC GLA n/a n/a
5 4WZE - NDG FUC GAL FUC n/a n/a
6 4OP7 - GLA FUC GLA n/a n/a
7 4X05 - GLA FUC GLA n/a n/a
8 4WZT - GLA FUC A2G n/a n/a
9 4X0C - NDG FUC GAL n/a n/a
10 4WZK - NDG GAL FUC n/a n/a
11 6H9V - MFU C7 H14 O5 C[C@H]1[C@....
12 4X07 - GLA FUC A2G n/a n/a
13 5LKC ic50 = 13 mM GLA FUC A2G n/a n/a
14 5LKG - GLC GAL FUC n/a n/a
15 6GW0 Kd = 0.000000064 M TUD C26 H45 N O6 S C[C@H](CCC....
16 6GVZ Kd = 0.4 uM CHO C26 H43 N O5 C[C@H](CCC....
17 4Z4W - FUL C6 H12 O5 C[C@H]1[C@....
18 6GW1 Kd = 0.000000064 M CHO C26 H43 N O5 C[C@H](CCC....
19 4Z4Z - GLA FUC GLA n/a n/a
20 3ONY - FUC C6 H12 O5 C[C@H]1[C@....
21 3Q3A - NAG GAL FUL n/a n/a
22 4Z4T - FUL C6 H12 O5 C[C@H]1[C@....
23 4Z4V - FUL C6 H12 O5 C[C@H]1[C@....
24 4Z4Y - GLA FUC GLA n/a n/a
25 5BSY - FLC C6 H5 O7 C(C(=O)[O-....
26 5HZB ic50 = 5.5 mM GLC GAL FUC n/a n/a
27 3PA2 - NAG FUC GAL FUC n/a n/a
28 4Z4S - FUL C6 H12 O5 C[C@H]1[C@....
29 3Q38 - GAL FUC GLA n/a n/a
30 3RY8 Kd = 460 uM FLC C6 H5 O7 C(C(=O)[O-....
31 3PA1 - GAL FUC A2G n/a n/a
32 6GW2 Kd = 0.0000123 M TUD C26 H45 N O6 S C[C@H](CCC....
33 4Z4U - FUL C6 H12 O5 C[C@H]1[C@....
34 3Q39 - GAL FUC n/a n/a
35 5HZA ic50 = 5.6 mM BGC FUC GAL n/a n/a
36 5BSX - FLC C6 H5 O7 C(C(=O)[O-....
37 6GY9 - KBA C10 H17 N3 O5 C[C@H]1[C@....
38 4Z4R - FUL C6 H12 O5 C[C@H]1[C@....
39 4RM0 - NAG GAL FUC n/a n/a
40 3PUN - NDG FUC GAL FUC n/a n/a
41 3PVD - NDG FUC GAL SIA n/a n/a
42 6JYN - NAG GAL n/a n/a
43 6JYS - A2G THR GAL NAG n/a n/a
44 4RDL - NDG FUC GAL FUC n/a n/a
45 4RDK - NDG GAL FUC FUC n/a n/a
46 3R6K - GAL FUC GLA n/a n/a
47 5N7M - GLC GAL FUC n/a n/a
48 2ZL6 - BGC GAL NAG GAL FUC n/a n/a
49 2ZL7 - GAL FUC NGA n/a n/a
50 3D26 - GAL FUC NGA n/a n/a
51 6IS5 - GLC GAL FUC A2G n/a n/a
52 4P25 - NAG FUC GAL FUC n/a n/a
53 4P3I - NAG GAL FUC n/a n/a
54 4P2N - NAG FUC GAL n/a n/a
55 4P26 - NAG GAL FUC A2G n/a n/a
56 4P1V - NAG GAL FUC n/a n/a
57 6GW4 Kd = 0.000000064 M CHO C26 H43 N O5 C[C@H](CCC....
58 2OBS - GL0 FUC A2G n/a n/a
59 2OBT - GAL FUC GLA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG FUC GAL; Similar ligands found: 115
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG FUC GAL 1 1
2 NAG GAL FUC FUC 0.8 0.978723
3 NDG FUC GAL FUC 0.8 0.978723
4 MAG SGA FUC 0.717949 0.730159
5 GAL NAG FUC GAL 0.679487 1
6 NAG FUC GAL FUC A2G 0.674699 0.938776
7 NAG GAL FUC FUC A2G 0.674699 0.938776
8 BGC FUC GAL 0.652174 0.73913
9 GLC BGC FUC GAL 0.652174 0.73913
10 NAG FUC 0.637681 0.978261
11 GLA NAG FUC GAL 0.626506 0.978723
12 NAG GAL FUC 0.61039 1
13 NAG GAL FUC GLA 0.609756 1
14 A2G GAL 0.608696 0.978261
15 NAG GAL FUC A2G 0.597403 1
16 MAG GAL FUC FUC 0.594937 0.958333
17 MAG FUC GAL FUC 0.594937 0.958333
18 NAG GAL 0.585714 0.978261
19 BGC FUC GAL NAG GAL 0.566667 1
20 GAL NAG GAL FUC FUC 0.551724 0.978723
21 BGC FUC GAL NAG 0.551724 1
22 GAL FUC GAL 0.547945 0.73913
23 MAG FUC G4S 0.546512 0.692308
24 MAG FUC SGA 0.54023 0.692308
25 NAG FUC GAL SIA 0.538462 0.884615
26 BGC GAL NAG GAL FUC FUC 0.531915 0.978723
27 GAL FUC A2G 0.530864 1
28 NAG GAL GAL 0.518987 0.978261
29 BGC FUC GAL FUC A2G 0.511111 0.978723
30 NDG GLA NAG GLC RAM 0.51 0.938776
31 NDG NAG GLA NAG GLC RAM 0.51 0.938776
32 NDG GLA GLC NAG GLC RAM 0.509804 0.938776
33 TVD GAL 0.5 0.938776
34 MGC GAL 0.5 0.978723
35 GLC GAL NAG GAL FUC GLA 0.494845 1
36 A2G GAL NAG 0.494118 0.958333
37 BGC GAL FUC GLA 0.493976 0.73913
38 BGC GAL NAG GAL FUC 0.489362 1
39 BGC GAL FUC A2G 0.48913 1
40 GLA NAG GAL FUC 0.488636 1
41 GLC GAL BGC FUC 0.487179 0.73913
42 BGC GAL FUC 0.487179 0.73913
43 A2G NAG 0.480519 0.958333
44 NAG NON FUC GAL FUC 0.474227 0.836364
45 NAG GAL NAG GAL NAG GAL 0.471264 0.938776
46 NAG GAL NAG GAL 0.471264 0.958333
47 BGC GAL NGA GAL 0.470588 0.978261
48 MAN NAG GAL 0.46988 0.978261
49 NAG GAL BGC GAL 0.465116 0.978261
50 A2G MBN GAL 0.465116 0.9375
51 NAG G6S 0.464286 0.714286
52 GAL NAG GAL 0.464286 0.978261
53 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.463918 0.92
54 NAG BMA 0.461538 0.88
55 AMU NAG 0.45977 0.92
56 BGC GAL NAG GAL 0.45977 0.978261
57 GAL NAG GAL FUC 0.456522 0.958333
58 NDG GAL FUC FUC 0.454545 0.9
59 C4W NAG FUC BMA 0.453608 0.884615
60 1GN ACY GAL 1GN BGC ACY GAL BGC 0.452632 0.958333
61 LOG GAL 0.444444 0.789474
62 GDL NAG 0.443038 0.958333
63 GLC GAL NAG GAL FUC A2G 0.442308 0.938776
64 HSH GLA FUC 0.44186 0.648148
65 A2G SER GAL 0.44186 0.865385
66 NGS FUC GLA SIA 0.440678 0.69697
67 BGC GAL GLA NGA GAL 0.43956 0.978261
68 FUC GAL 0.438356 0.717391
69 GAL NAG GAL NAG GAL 0.438202 0.958333
70 ASG GC4 0.433333 0.661538
71 GAL FUC 0.432432 0.702128
72 GAL A2G MBN 0.431818 0.918367
73 HSH A2G FUC 0.431579 0.836364
74 XYS GAL FUC 0.428571 0.723404
75 NAG TA5 FUC 0.428571 0.681818
76 NAG NAG BMA 0.426966 0.884615
77 NAG BDP 0.426829 0.897959
78 ASG GCD 0.423913 0.636364
79 BGC GAL NGA 0.423529 0.978261
80 NAG BMA MAN MAN MAN MAN 0.42268 0.978261
81 NOK GAL 0.421687 0.785714
82 NAG NAG NAG NAG NAG 0.421687 0.938776
83 NAG NAG NAG NAG NAG NAG NAG NAG 0.421687 0.938776
84 NDG NAG NAG NAG NAG 0.421687 0.938776
85 NAG NAG NAG NAG NAG NAG 0.421687 0.938776
86 A2G THR GAL 0.420455 0.901961
87 NAG GAL NAG 0.420455 0.958333
88 BMA MAN MAN MAN 0.418605 0.744681
89 MAG FUC GAL SIA 0.415929 0.849057
90 GCU BGC 0.415584 0.702128
91 C4W NAG FUC BMA MAN 0.415094 0.884615
92 GLC U8V 0.413333 0.744681
93 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.411765 0.978261
94 BHE 0.411765 0.648148
95 ASG IDR ASG IDR 0.41 0.692308
96 NAG NAG MAN MAN MAN 0.41 0.958333
97 BMA MAN NAG 0.409091 0.978261
98 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.407767 0.978261
99 GAL NAG FUC GAL SIA 0.40678 0.884615
100 4YA 0.404762 0.648148
101 GAL GC2 0.404494 0.676923
102 BGC GAL NAG 0.404494 0.978261
103 GAL GLA 0.402778 0.717391
104 AMU 0.402597 0.893617
105 GAL NAG 0.402439 0.978261
106 A2G NPO GAL 0.402174 0.703125
107 NAG BDP NAG BDP NAG BDP NAG 0.402062 0.92
108 MAN NAG 0.4 0.978261
109 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.4 0.717391
110 GLC GLC GLC GLC BGC GLC GLC 0.4 0.717391
111 MAN BMA BMA BMA BMA BMA BMA 0.4 0.717391
112 NAG BMA MAN MAN NAG GAL NAG GAL 0.4 0.938776
113 GAL FUC NGA 0.4 0.918367
114 NAG GAL GLC NAG GLC RAM 0.4 0.958333
115 NDG GAL 0.4 0.728814
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG FUC GAL; Similar ligands found: 4
No: Ligand Similarity coefficient
1 NDG FUC GAL 0.9753
2 MAG FUC GAL 0.9581
3 NDG GAL FUC 0.8990
4 NAG FUC SGA 0.8950
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P25; Ligand: NAG FUC GAL FUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4p25.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4P25; Ligand: NAG FUC GAL FUC; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4p25.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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