Receptor
PDB id Resolution Class Description Source Keywords
5F7N 2.28 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A LEWIS B PENTASACCHARIDE HELICOBACTER PYLORI ADHESIN LECTIN NANOBODY COMPLEX CELL ADHESION
Ref.: STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BIN HELICOBACTER PYLORI. CELL HOST MICROBE V. 19 55 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG GAL FUC FUC A2G A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
878.828 n/a O=C(N...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F7N 2.28 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A LEWIS B PENTASACCHARIDE HELICOBACTER PYLORI ADHESIN LECTIN NANOBODY COMPLEX CELL ADHESION
Ref.: STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BIN HELICOBACTER PYLORI. CELL HOST MICROBE V. 19 55 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG GAL FUC FUC A2G; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL FUC FUC A2G 1 1
2 FUC GAL NAG A2G FUC 0.95 1
3 BGC FUC GAL FUC A2G 0.77907 0.959184
4 GLC FUC GAL FUC A2G 0.77907 0.959184
5 A2G GAL NAG FUC 0.770115 1
6 A2G GAL BGC FUC 0.730337 0.938776
7 BCW 0.702381 0.959184
8 FUC NDG GAL FUC 0.702381 0.959184
9 FUC NAG GAL FUC 0.702381 0.959184
10 FUC GAL NAG FUC 0.702381 0.959184
11 GAL NAG FUC 0.674699 0.938776
12 FUC NAG GAL 0.674699 0.938776
13 GAL NDG FUC 0.674699 0.938776
14 FUC NDG GAL 0.674699 0.938776
15 FUC GAL NDG FUC 0.662791 0.959184
16 BDZ 0.662791 0.959184
17 GAL NAG FUC FUC 0.662791 0.959184
18 GAL NDG FUC FUC 0.662791 0.959184
19 FUC GAL A2G 0.658824 0.938776
20 NGA GAL FUC 0.658824 0.938776
21 A2G GAL FUC 0.658824 0.938776
22 FUC GLA A2G 0.658824 0.938776
23 A2G GLA FUC 0.658824 0.938776
24 FUC GL0 A2G 0.658824 0.938776
25 GLC GAL NAG GAL FUC A2G 0.637255 1
26 A2G GAL NAG FUC GAL GLC 0.637255 1
27 FUC BGC GAL NAG 0.634409 0.938776
28 BGA 0.614583 0.824561
29 NAG NGA 0.559524 0.979592
30 NAG A2G 0.559524 0.979592
31 NAG GAL FUC 0.549451 0.938776
32 DR3 0.549451 0.938776
33 GLA GAL NAG FUC GAL GLC 0.542857 0.938776
34 FUC GAL MAG FUC 0.537634 0.94
35 FUC GAL NAG GAL FUC 0.535354 0.959184
36 NAG MUB 0.531915 0.98
37 NAG AMU 0.531915 0.98
38 FUC NAG 0.529412 0.918367
39 FUL GAL NAG 0.521739 0.938776
40 DR2 0.521739 0.938776
41 NDG GAL FUC 0.521739 0.938776
42 FUC GAL NDG 0.521739 0.938776
43 FUC GAL NAG 0.521739 0.938776
44 FUC BGC GAL NAG GAL 0.519231 0.938776
45 BGC GLA GAL FUC 0.516129 0.693878
46 MAG FUC GAL 0.51087 0.94
47 GLA NAG GAL FUC 0.510204 0.938776
48 GAL NAG GAL FUC 0.510204 0.938776
49 NAG GDL 0.505747 0.979592
50 CBS CBS 0.505747 0.979592
51 CBS 0.505747 0.979592
52 NAG NDG 0.505747 0.979592
53 GLC GAL NAG GAL FUC FUC 0.504673 0.959184
54 BGC GAL NAG GAL FUC FUC 0.504673 0.959184
55 NAG GAL NAG 0.494737 0.979592
56 NAG FUC 0.494253 0.897959
57 NAG GCU NAG GCU NAG GCU 5AX 0.485437 0.98
58 NAG BDP NAG BDP NAG BDP NAG 0.485437 0.98
59 NAG NAG NAG NAG NDG NAG 0.483516 1
60 NDG NAG NAG NDG 0.483516 1
61 CTO 0.483516 1
62 NDG NAG NAG 0.483516 1
63 NDG NAG NAG NAG 0.483516 1
64 NAG NAG NAG NAG 0.483516 1
65 NAG NAG NAG NAG NAG NAG NAG NAG 0.483516 1
66 NAG NAG NAG 0.483516 1
67 NAG NAG NAG NAG NAG NAG 0.483516 1
68 NAG NAG NAG NAG NDG 0.483516 1
69 NAG NAG NAG NDG 0.483516 1
70 NDG NAG NAG NDG NAG 0.483516 1
71 NAG NAG NAG NAG NAG 0.483516 1
72 NAG NAG NDG 0.483516 1
73 NAG GAL 0.477273 0.918367
74 GAL NAG 0.477273 0.918367
75 NGA GAL 0.477273 0.918367
76 FUC BGC GAL 0.47191 0.693878
77 SGA MAG FUC 0.470588 0.71875
78 NGA GAL BGC 0.468085 0.918367
79 FUC GAL NAG GAL BGC 0.46729 0.938776
80 MAN NAG 0.465909 0.918367
81 NAG MU2 0.464912 0.890909
82 NAG GAL BGC 0.463918 0.918367
83 NAG FUC SIA GAL 0.46281 0.942308
84 SIA GAL NDG FUC 0.46281 0.942308
85 NDG FUC SIA GAL 0.46281 0.942308
86 SIA GLA NAG FUC 0.46281 0.942308
87 SIA GAL NAG FUC 0.46281 0.942308
88 FUC NDG GAL SIA 0.46281 0.942308
89 FUC NAG GLA GAL 0.461538 0.92
90 NAG MAN MMA 0.458333 0.92
91 NAG MBG 0.455556 0.92
92 NGA GLA GAL BGC 0.455446 0.918367
93 MBG A2G 0.450549 0.92
94 A2G MBG 0.450549 0.92
95 MAN MAN NAG 0.44898 0.882353
96 FUC GAL NAG A2G 0.448598 0.907407
97 G4S MAG FUC 0.446602 0.71875
98 NDG NAG 0.445652 1
99 FUC GLA GLA 0.444444 0.693878
100 NAG AMU ALA DGL 0.444444 0.907407
101 GLA GLA FUC 0.444444 0.693878
102 GLA GAL FUC 0.444444 0.693878
103 GAL GAL FUC 0.444444 0.693878
104 FUC GAL GLA 0.444444 0.693878
105 A2G GAL 0.438202 0.918367
106 GAL A2G 0.438202 0.918367
107 GAL NGA 0.438202 0.918367
108 RAM GLC GAL NAG NAG GLC 0.4375 0.942308
109 GAL NGA A2G 0.43617 0.96
110 NAG NM9 0.434343 0.960784
111 NAG NGO 0.43299 0.87037
112 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.432432 0.98
113 NAG MAN BMA 0.43 0.918367
114 NAG MAN MAN 0.43 0.918367
115 NAG MAN MAN MAN NAG 0.428571 0.979592
116 3QL 0.42268 0.90566
117 NAG BMA NAG MAN MAN NAG NAG 0.422414 1
118 NAG GAL GAL NAG 0.421569 0.979592
119 GAL NAG GAL NAG GAL NAG 0.421569 1
120 NAG NAG 0.421053 0.886792
121 NAG MAN BMA NDG MAN NAG GAL 0.420168 1
122 M5G 0.416667 0.979592
123 FUC GAL NAG NON FUC 0.415929 0.857143
124 FUC GAL NGA 0.415842 0.88
125 BGB 0.415842 0.614035
126 NAG NAG NAG NAG NAG NAG NAG 0.415094 0.907407
127 GLC GAL FUC 0.414894 0.693878
128 BGC GAL FUC 0.414894 0.693878
129 FUC LAT 0.414894 0.693878
130 FUC GAL GLC 0.414894 0.693878
131 LAT FUC 0.414894 0.693878
132 MMA MAN NAG MAN NAG NAG 0.407407 0.98
133 GAL NDG 0.406593 0.918367
134 NLC 0.406593 0.918367
135 NDG GAL 0.406593 0.918367
136 LEC NGA 0.40566 0.765625
137 WZ5 0.401786 0.92
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F7N; Ligand: NAG GAL FUC FUC A2G; Similar sites found: 25
This union binding pocket(no: 1) in the query (biounit: 5f7n.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FE2 AIR 0.01276 0.41348 2.7451
2 4DSU BZI 0.001623 0.47324 3.1746
3 2VDF OCT 0.0001066 0.53033 3.33333
4 5F7J ADE 0.01256 0.42578 4.16667
5 5IFK HPA 0.02899 0.40525 4.16667
6 5D9G GLU ASN LEU TYR PHE GLN 0.01216 0.41877 5.83333
7 4XMF HSM 0.01847 0.40382 5.97826
8 3AB4 THR 0.02131 0.40243 6.17978
9 5MRH Q9Z 0.02491 0.40292 6.66667
10 4BTV RB3 0.03416 0.4018 6.66667
11 4WOE ADP 0.01968 0.41408 7.5
12 1JJV ATP 0.02628 0.40836 7.5
13 4KBA 1QM 0.02512 0.40273 7.5
14 5EWK P34 0.01737 0.41695 8
15 2QHV OC9 0.007357 0.42982 8.33333
16 2QHS OCA 0.00787 0.42384 8.33333
17 2WBV SIA 0.03915 0.41228 8.46561
18 3A16 PXO 0.002422 0.48018 9.16667
19 3LL5 IP8 0.03219 0.40366 10.8434
20 3UYW TAU 0.02996 0.41105 13.5514
21 2JK0 ASP 0.02615 0.40654 14.1667
22 4PAB THG 0.005166 0.41653 15
23 5MX4 HPA 0.008348 0.43336 15.4506
24 2G30 ALA ALA PHE 0.000141 0.51056 20.8333
25 2PNC CLU 0.02617 0.41142 21.6667
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