Receptor
PDB id Resolution Class Description Source Keywords
5F8R 2.44 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL S831 IN COMPLEX WITH BLOOD GROUP H LEWIS B HEXASACCHARIDE 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
BGC GAL NAG GAL FUC FUC A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
999.916 n/a O=C(N...
View in 3D viewer
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: BGC GAL NAG GAL FUC FUC; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL NAG GAL FUC FUC 1 1
2 GLC GAL NAG GAL FUC FUC 1 1
3 FUC GAL NAG GAL BGC 0.840909 0.978723
4 FUC GAL NAG GAL FUC 0.764045 1
5 GLA GAL NAG FUC GAL GLC 0.704082 0.978723
6 GLC GAL NAG GAL FUC A2G 0.669903 0.959184
7 A2G GAL NAG FUC GAL GLC 0.669903 0.959184
8 GLA NAG GAL FUC 0.663043 0.978723
9 GAL NAG GAL FUC 0.663043 0.978723
10 GAL NAG GAL BGC 0.655556 0.957447
11 BGC GAL NAG GAL 0.655556 0.957447
12 LAT NAG GAL 0.655556 0.957447
13 FUC BGC GAL NAG GAL 0.646465 0.978723
14 FUC GAL MAG FUC 0.644444 0.979167
15 FUC GAL GLC 0.642857 0.723404
16 FUC LAT 0.642857 0.723404
17 GLC GAL FUC 0.642857 0.723404
18 BGC GAL FUC 0.642857 0.723404
19 LAT FUC 0.642857 0.723404
20 GLC GAL NAG GAL 0.641304 0.957447
21 GAL NGA GLA BGC GAL 0.62766 0.957447
22 FUC NDG GAL FUC 0.626374 1
23 FUC GAL NAG FUC 0.626374 1
24 FUC NAG GAL FUC 0.626374 1
25 BCW 0.626374 1
26 NAG GAL BGC 0.615385 0.957447
27 FUC BGC GAL NAG 0.602041 0.978723
28 NGA GLA GAL BGC 0.6 0.957447
29 DR2 0.593407 0.978723
30 FUL GAL NAG 0.593407 0.978723
31 FUC GAL NAG 0.593407 0.978723
32 FUC GAL NDG 0.593407 0.978723
33 NDG GAL FUC 0.593407 0.978723
34 GAL NAG FUC FUC 0.591398 1
35 BDZ 0.591398 1
36 GAL NDG FUC FUC 0.591398 1
37 FUC GAL NDG FUC 0.591398 1
38 A2G GAL BGC FUC 0.59 0.978723
39 DR3 0.553191 0.978723
40 NAG GAL FUC 0.553191 0.978723
41 BGC GLA GAL FUC 0.553191 0.723404
42 MAG FUC GAL 0.548387 0.979167
43 FUC NAG GLA GAL 0.539216 0.958333
44 GLA GAL GAL 0.534884 0.702128
45 GLA GAL BGC 0.534884 0.702128
46 SGA MAG FUC 0.534653 0.741935
47 FUC NDG GAL 0.531915 0.978723
48 FUC NAG GAL 0.531915 0.978723
49 GAL NAG FUC 0.531915 0.978723
50 GAL NDG FUC 0.531915 0.978723
51 NAG GAL GAL NAG GAL 0.530612 0.938776
52 GAL NAG GAL NAG GAL NAG 0.530612 0.959184
53 NAG GAL GAL NAG 0.530612 0.938776
54 NAG GAL GAL 0.526882 0.957447
55 MAN BMA NAG 0.526882 0.957447
56 GLA GAL NAG 0.526882 0.957447
57 FUC GAL NAG A2G 0.52381 0.87037
58 FUC GAL NAG NON FUC 0.513761 0.854545
59 BGC BGC BGC BGC 0.511111 0.702128
60 BGC BGC BGC BGC BGC BGC BGC BGC 0.511111 0.702128
61 NAG GAL FUC FUC A2G 0.504673 0.959184
62 NAG GAL NAG 0.5 0.938776
63 NAG FUC 0.5 0.93617
64 NAG MAN GAL BMA NAG MAN NAG GAL 0.495575 0.959184
65 MAN BMA NAG NAG MAN NAG GAL GAL 0.495575 0.959184
66 NAG MAN MAN MAN NAG GAL NAG GAL 0.495575 0.959184
67 NAG MAN GAL BMA NDG MAN NAG GAL 0.495575 0.959184
68 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.495495 0.957447
69 GLC FUC GAL FUC A2G 0.490566 1
70 BGC FUC GAL FUC A2G 0.490566 1
71 NGA GAL BGC 0.489583 0.957447
72 A2G GAL NAG FUC 0.485981 0.959184
73 G4S MAG FUC 0.480769 0.741935
74 FUC BGC GAL 0.478261 0.723404
75 FUC GAL NAG A2G FUC 0.477064 0.959184
76 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.475 0.938776
77 NAG MAN BMA NDG MAN NAG GAL 0.474576 0.959184
78 MAN MAN MAN GLC 0.473118 0.702128
79 NAG MAN GAL MAN MAN NAG GAL 0.468468 0.938776
80 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.464286 0.94
81 M5G 0.458333 0.938776
82 GAL NAG MAN 0.454545 0.957447
83 MAN NAG GAL 0.454545 0.957447
84 NAG BMA NAG MAN MAN NAG NAG 0.452991 0.959184
85 SIA GAL NAG GAL GLC 0.450382 0.886792
86 SIA GAL NAG GAL BGC 0.450382 0.886792
87 BGC GAL NAG SIA GAL 0.450382 0.886792
88 NAG MAN MMA 0.45 0.958333
89 NAG NAG BMA MAN 0.449541 0.867925
90 BMA BMA 0.447059 0.702128
91 GAL GLC 0.447059 0.702128
92 CBK 0.447059 0.702128
93 GLA GAL 0.447059 0.702128
94 MAB 0.447059 0.702128
95 B2G 0.447059 0.702128
96 GAL BGC 0.447059 0.702128
97 BMA GAL 0.447059 0.702128
98 MAL MAL 0.447059 0.6875
99 BGC BMA 0.447059 0.702128
100 BGC GAL 0.447059 0.702128
101 GLC GAL 0.447059 0.702128
102 MAL 0.447059 0.702128
103 LAT 0.447059 0.702128
104 GLC BGC 0.447059 0.702128
105 CBI 0.447059 0.702128
106 BGC GLC 0.447059 0.702128
107 GLA GLA 0.447059 0.702128
108 LBT 0.447059 0.702128
109 N9S 0.447059 0.702128
110 BGC GAL SIA NGA GAL 0.446154 0.903846
111 GAL NGA GAL BGC SIA 0.446154 0.903846
112 GAL NGA SIA GAL BGC 0.446154 0.903846
113 SIA GAL BGC NGA GAL 0.446154 0.903846
114 GAL NDG 0.445652 0.957447
115 NLC 0.445652 0.957447
116 NDG GAL 0.445652 0.957447
117 FUC GAL A2G 0.445545 0.978723
118 A2G GLA FUC 0.445545 0.978723
119 NGA GAL FUC 0.445545 0.978723
120 A2G GAL FUC 0.445545 0.978723
121 FUC GL0 A2G 0.445545 0.978723
122 FUC GLA A2G 0.445545 0.978723
123 NAG NAG BMA MAN MAN MAN MAN 0.443548 0.867925
124 FUC NAG 0.43617 0.957447
125 BMA MAN MAN 0.434783 0.702128
126 XYS GAL FUC 0.434343 0.708333
127 GLA MAN RAM RAM ABE MAN GLA 0.433333 0.734694
128 NAG NAG BMA MAN MAN 0.429825 0.938776
129 MAN MAN NAG MAN NAG 0.429825 0.938776
130 NAG BMA MAN MAN MAN MAN 0.427273 0.957447
131 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.426966 0.702128
132 CTT 0.426966 0.702128
133 GLC GLC BGC GLC GLC GLC GLC 0.426966 0.702128
134 CT3 0.426966 0.702128
135 BGC BGC BGC GLC 0.426966 0.702128
136 GLC BGC GLC 0.426966 0.702128
137 GLC BGC BGC BGC BGC BGC 0.426966 0.702128
138 BMA BMA BMA BMA BMA 0.426966 0.702128
139 BGC GLC GLC GLC 0.426966 0.702128
140 CTR 0.426966 0.702128
141 BGC BGC BGC BGC BGC BGC 0.426966 0.702128
142 GAL GAL GAL 0.426966 0.702128
143 BGC GLC GLC GLC GLC GLC GLC 0.426966 0.702128
144 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.426966 0.702128
145 BMA MAN BMA 0.426966 0.702128
146 GLC GLC BGC 0.426966 0.702128
147 BMA BMA BMA 0.426966 0.702128
148 MLR 0.426966 0.702128
149 MTT 0.426966 0.702128
150 CEX 0.426966 0.702128
151 B4G 0.426966 0.702128
152 GLA GAL GLC 0.426966 0.702128
153 BMA BMA BMA BMA BMA BMA 0.426966 0.702128
154 GLC GLC GLC GLC GLC GLC GLC GLC 0.426966 0.702128
155 BGC GLC GLC GLC GLC 0.426966 0.702128
156 CE5 0.426966 0.702128
157 MAN BMA BMA 0.426966 0.702128
158 MT7 0.426966 0.702128
159 CE8 0.426966 0.702128
160 BGC GLC GLC 0.426966 0.702128
161 GLC GLC GLC GLC GLC 0.426966 0.702128
162 MAN MAN BMA BMA BMA BMA 0.426966 0.702128
163 MAN BMA BMA BMA BMA 0.426966 0.702128
164 GLC GLC GLC GLC GLC GLC GLC 0.426966 0.702128
165 CE6 0.426966 0.702128
166 DXI 0.426966 0.702128
167 GLC BGC BGC BGC BGC 0.426966 0.702128
168 CEY 0.426966 0.702128
169 GLC GAL GAL 0.426966 0.702128
170 GLC BGC BGC 0.426966 0.702128
171 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.425 0.882353
172 ABD 0.420561 0.93617
173 BGC GAL SIA SIA GAL NGA 0.416667 0.903846
174 GAL BGC GAL SIA NGA SIA 0.416667 0.903846
175 G6D GLC ACI GLD GLC ACI GLD GLC BGC 0.413793 0.788462
176 OPM MAN MAN 0.411765 0.62963
177 SLT 0.411765 0.92
178 FUC GAL 0.411111 0.702128
179 SIA GAL MAG FUC 0.410853 0.867925
180 ACG 0.410256 0.84
181 GAL BGC NAG GAL 0.409524 0.957447
182 MAN BMA BMA BMA BMA BMA 0.408602 0.6875
183 BMA BMA BMA BMA BMA BMA MAN 0.408602 0.6875
184 GAL GAL FUC 0.40625 0.723404
185 FUC GLA GLA 0.40625 0.723404
186 GLA GLA FUC 0.40625 0.723404
187 FUC GAL GLA 0.40625 0.723404
188 GLA GAL FUC 0.40625 0.723404
189 GLC ACI GLD GLC 0.405405 0.816327
190 GLC G6D ACI GLC 0.405405 0.816327
191 GLC G6D ADH GLC 0.405405 0.816327
192 GLC ACI G6D BGC 0.405405 0.816327
193 SIA GAL GLC 0.404959 0.901961
194 SIA BGC GAL 0.404959 0.901961
195 GLA GLC SIA 0.404959 0.901961
196 BGC GAL SIA 0.404959 0.901961
197 SIA GAL BGC 0.404959 0.901961
198 BGC SIA GAL 0.404959 0.901961
199 GAL BGC SIA 0.404959 0.901961
200 NAG NAG BMA MAN MAN NAG NAG 0.404762 0.886792
201 1GN ACY GAL ACY 1GN BGC GAL BGC 0.403509 0.938776
202 GLC ACI G6D GLC 0.403509 0.803922
203 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.403509 0.938776
204 GLC ACI GLD GAL 0.403509 0.803922
205 MAN MAN BMA 0.402174 0.702128
206 GAL NGA GAL SIA 0.401575 0.903846
207 SIA GAL NGA GAL 0.401575 0.903846
208 NAG FUC SIA GAL 0.4 0.903846
209 SIA GLA NAG FUC 0.4 0.903846
210 GAL MGC 0.4 0.958333
211 NDG FUC SIA GAL 0.4 0.903846
212 SIA GAL NDG FUC 0.4 0.903846
213 8VZ 0.4 0.92
214 SIA GAL NAG FUC 0.4 0.903846
215 FUC NDG GAL SIA 0.4 0.903846
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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