Receptor
PDB id Resolution Class Description Source Keywords
5F7Y 2.44 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A TYPE-1 HEXASACCHARIDE HELICOBACTER PYLORI CELL ADHESION ADHESIN LECTIN NANOBODY COMPLEX
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
GLC GAL NAG GAL FUC A2G A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
1056.97 n/a O=C(N...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F7Y 2.44 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A TYPE-1 HEXASACCHARIDE HELICOBACTER PYLORI CELL ADHESION ADHESIN LECTIN NANOBODY COMPLEX
Ref.: STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BIN HELICOBACTER PYLORI. CELL HOST MICROBE V. 19 55 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 5F7Y - GLC GAL NAG GAL FUC A2G n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 5F7Y - GLC GAL NAG GAL FUC A2G n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 5F7Y - GLC GAL NAG GAL FUC A2G n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLC GAL NAG GAL FUC A2G; Similar ligands found: 223
No: Ligand ECFP6 Tc MDL keys Tc
1 A2G GAL NAG FUC GAL GLC 1 1
2 GLC GAL NAG GAL FUC A2G 1 1
3 GLA GAL NAG FUC GAL GLC 0.880435 0.938776
4 A2G GAL BGC FUC 0.833333 0.938776
5 FUC GAL NAG GAL BGC 0.787234 0.938776
6 NAG GAL BGC 0.719101 0.918367
7 NGA GLA GAL BGC 0.698925 0.918367
8 GLC FUC GAL FUC A2G 0.690722 0.959184
9 BGC FUC GAL FUC A2G 0.690722 0.959184
10 LAT NAG GAL 0.684783 0.918367
11 BGC GAL NAG GAL 0.684783 0.918367
12 GAL NAG GAL BGC 0.684783 0.918367
13 A2G GAL NAG FUC 0.683673 1
14 FUC BGC GAL NAG 0.680412 0.938776
15 GLC GAL NAG GAL FUC FUC 0.669903 0.959184
16 BGC GAL NAG GAL FUC FUC 0.669903 0.959184
17 GAL NGA GLA BGC GAL 0.65625 0.918367
18 NAG GAL FUC FUC A2G 0.637255 1
19 FUC GAL NAG A2G FUC 0.637255 1
20 BGC GLA GAL FUC 0.634409 0.693878
21 GLC GAL NAG GAL 0.618557 0.918367
22 FUC BGC GAL NAG GAL 0.609524 0.938776
23 NGA GAL BGC 0.585106 0.918367
24 FUC GLA A2G 0.583333 0.938776
25 NGA GAL FUC 0.583333 0.938776
26 FUC GL0 A2G 0.583333 0.938776
27 A2G GLA FUC 0.583333 0.938776
28 FUC GAL A2G 0.583333 0.938776
29 A2G GAL FUC 0.583333 0.938776
30 NAG GAL NAG 0.57732 0.979592
31 BGA 0.551402 0.824561
32 GLC GAL FUC 0.515789 0.693878
33 FUC LAT 0.515789 0.693878
34 LAT FUC 0.515789 0.693878
35 FUC GAL GLC 0.515789 0.693878
36 BGC GAL FUC 0.515789 0.693878
37 GAL NAG GAL NAG GAL NAG 0.514563 1
38 NAG GAL GAL NAG 0.514563 0.979592
39 NAG GAL GAL NAG GAL 0.514563 0.979592
40 GAL NAG GAL FUC 0.5 0.938776
41 GLA GAL GAL 0.5 0.673469
42 GLA GAL BGC 0.5 0.673469
43 GLA NAG GAL FUC 0.5 0.938776
44 FUC GAL NAG GAL FUC 0.495413 0.959184
45 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.491228 0.98
46 DR3 0.490196 0.938776
47 NAG GAL FUC 0.490196 0.938776
48 NAG MAN BMA NDG MAN NAG GAL 0.487603 1
49 GAL NAG 0.484211 0.918367
50 NAG GAL 0.484211 0.918367
51 NGA GAL 0.484211 0.918367
52 M5G 0.483607 0.979592
53 DR2 0.480392 0.938776
54 FUL GAL NAG 0.480392 0.938776
55 NAG MAN MMA 0.480392 0.92
56 FUC GAL NDG 0.480392 0.938776
57 NDG GAL FUC 0.480392 0.938776
58 FUC GAL NAG 0.480392 0.938776
59 GLA GAL NAG 0.48 0.918367
60 NAG GAL GAL 0.48 0.918367
61 MAN BMA NAG 0.48 0.918367
62 BGC BGC BGC BGC BGC BGC BGC BGC 0.479167 0.673469
63 NAG MBG 0.479167 0.92
64 BGC BGC BGC BGC 0.479167 0.673469
65 NAG BMA NAG MAN MAN NAG NAG 0.466667 1
66 GLA MAN RAM ABE GLA MAN RAM ABE 0.457627 0.705882
67 GLA MAN RAM TYV GLA MAN RAM TYV 0.457627 0.705882
68 NAG FUC 0.453608 0.897959
69 NAG BDP NAG BDP NAG BDP NAG 0.451327 0.98
70 NAG GCU NAG GCU NAG GCU 5AX 0.451327 0.98
71 CBS CBS 0.44898 0.979592
72 CBS 0.44898 0.979592
73 NAG GDL 0.44898 0.979592
74 NAG NGA 0.44898 0.979592
75 NAG A2G 0.44898 0.979592
76 NAG NDG 0.44898 0.979592
77 GLA MAN RAM RAM ABE MAN GLA 0.447154 0.705882
78 NAG MAN GAL BMA NDG MAN NAG GAL 0.446281 1
79 NAG MAN GAL BMA NAG MAN NAG GAL 0.446281 1
80 MAN BMA NAG NAG MAN NAG GAL GAL 0.446281 1
81 NAG MAN MAN MAN NAG GAL NAG GAL 0.446281 1
82 A2G MBG 0.444444 0.92
83 MBG A2G 0.444444 0.92
84 MAN NAG 0.443299 0.918367
85 GAL NDG FUC 0.442308 0.938776
86 FUC NAG GAL 0.442308 0.938776
87 GAL NAG FUC 0.442308 0.938776
88 FUC NDG GAL 0.442308 0.938776
89 BGC GAL NAG SIA GAL 0.441176 0.924528
90 SIA GAL NAG GAL GLC 0.441176 0.924528
91 SIA GAL NAG GAL BGC 0.441176 0.924528
92 BDZ 0.439252 0.959184
93 BCW 0.439252 0.959184
94 GAL NAG FUC FUC 0.439252 0.959184
95 FUC NAG GAL FUC 0.439252 0.959184
96 FUC NDG GAL FUC 0.439252 0.959184
97 GAL NDG FUC FUC 0.439252 0.959184
98 FUC GAL NDG FUC 0.439252 0.959184
99 FUC GAL NAG FUC 0.439252 0.959184
100 FUC NAG 0.438776 0.918367
101 NAG NAG BMA MAN 0.438596 0.90566
102 FUC BGC GAL 0.434343 0.693878
103 NDG NAG NAG NDG 0.431373 1
104 NDG NAG NAG 0.431373 1
105 NAG NAG NAG NAG NAG NAG NAG NAG 0.431373 1
106 CTO 0.431373 1
107 NAG NAG NAG NAG NDG 0.431373 1
108 NAG NAG NAG 0.431373 1
109 NAG NAG NAG NAG 0.431373 1
110 NAG NAG NAG NAG NAG NAG 0.431373 1
111 NDG NAG NAG NAG 0.431373 1
112 NAG NAG NAG NAG NDG NAG 0.431373 1
113 NAG NAG NDG 0.431373 1
114 NAG NAG NAG NDG 0.431373 1
115 NDG NAG NAG NDG NAG 0.431373 1
116 NAG NAG NAG NAG NAG 0.431373 1
117 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.431034 0.979592
118 1GN ACY GAL ACY 1GN BGC GAL BGC 0.431034 0.979592
119 FUC GAL NAG A2G 0.431034 0.907407
120 MAG FUC GAL 0.428571 0.94
121 GAL NAG MAN 0.428571 0.918367
122 MAN NAG GAL 0.428571 0.918367
123 GAL NGA GAL BGC SIA 0.426471 0.942308
124 SIA GAL BGC NGA GAL 0.426471 0.942308
125 BGC GAL SIA NGA GAL 0.426471 0.942308
126 GAL NGA SIA GAL BGC 0.426471 0.942308
127 FUC GAL MAG FUC 0.425926 0.94
128 NAG MAN BMA 0.425926 0.918367
129 NAG MAN MAN 0.425926 0.918367
130 NAG MAN MAN MAN NAG 0.424779 0.979592
131 SGA MAG FUC 0.424779 0.71875
132 GLA GLA FUC 0.424242 0.693878
133 GLA GAL FUC 0.424242 0.693878
134 FUC GAL GLA 0.424242 0.693878
135 GAL GAL FUC 0.424242 0.693878
136 FUC GLA GLA 0.424242 0.693878
137 SIA GAL BGC NGA 0.421053 0.942308
138 GAL BGC SIA NGA 0.421053 0.942308
139 BGC GAL SIA NGA 0.421053 0.942308
140 NAG MAN GAL MAN MAN NAG GAL 0.420168 0.979592
141 NAG NAG BMA MAN MAN 0.420168 0.979592
142 MAN MAN NAG MAN NAG 0.420168 0.979592
143 NAG NAG BMA MAN MAN NAG NAG 0.418605 0.924528
144 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.418605 0.979592
145 BGC GLC 0.417582 0.673469
146 N9S 0.417582 0.673469
147 GAL GLC 0.417582 0.673469
148 MAL 0.417582 0.673469
149 CBK 0.417582 0.673469
150 GLA GAL 0.417582 0.673469
151 MAL MAL 0.417582 0.66
152 LAT 0.417582 0.673469
153 BGC BMA 0.417582 0.673469
154 MAB 0.417582 0.673469
155 GAL BGC 0.417582 0.673469
156 BMA BMA 0.417582 0.673469
157 GLC GAL 0.417582 0.673469
158 CBI 0.417582 0.673469
159 GLC BGC 0.417582 0.673469
160 GLA GLA 0.417582 0.673469
161 BMA GAL 0.417582 0.673469
162 LBT 0.417582 0.673469
163 B2G 0.417582 0.673469
164 BGC GAL 0.417582 0.673469
165 MAN MAN NAG 0.416667 0.882353
166 GLA MAN RAM ABE 0.415929 0.686275
167 SIA GAL NGA GAL 0.415385 0.942308
168 GAL NGA GAL SIA 0.415385 0.942308
169 GLA MAN RAM TYV GLA MAN GLC RAM TYV 0.41129 0.705882
170 ABD 0.410714 0.897959
171 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.409836 0.918367
172 FUC NAG GLA GAL 0.405172 0.92
173 GAL MGC 0.40404 0.92
174 NLC 0.40404 0.918367
175 NDG GAL 0.40404 0.918367
176 GAL NDG 0.40404 0.918367
177 RAM GLC GAL NAG NAG GLC 0.402878 0.942308
178 NAG NGO 0.401869 0.87037
179 ACG 0.401639 0.807692
180 MTT 0.4 0.673469
181 GLC GAL GAL 0.4 0.673469
182 GLC GLC GLC GLC GLC GLC GLC 0.4 0.673469
183 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.673469
184 CT3 0.4 0.673469
185 GLC GLC BGC GLC GLC GLC GLC 0.4 0.673469
186 BGC GLC GLC 0.4 0.673469
187 MAN BMA BMA BMA BMA 0.4 0.673469
188 MAN MAN BMA BMA BMA BMA 0.4 0.673469
189 GAL GAL GAL 0.4 0.673469
190 GLC GLC BGC 0.4 0.673469
191 BGC GLC GLC GLC GLC 0.4 0.673469
192 CEX 0.4 0.673469
193 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.4 0.673469
194 BMA BMA BMA BMA BMA 0.4 0.673469
195 B4G 0.4 0.673469
196 BGB 0.4 0.614035
197 BMA MAN BMA 0.4 0.673469
198 BMA BMA BMA BMA BMA BMA 0.4 0.673469
199 CE6 0.4 0.673469
200 GLC BGC BGC BGC BGC 0.4 0.673469
201 BGC GLC GLC GLC GLC GLC GLC 0.4 0.673469
202 CE8 0.4 0.673469
203 WZ5 0.4 0.92
204 SIA GAL SIA BGC NGA 0.4 0.924528
205 MT7 0.4 0.673469
206 GLA GAL GLC 0.4 0.673469
207 CEY 0.4 0.673469
208 BGC BGC BGC GLC 0.4 0.673469
209 GLC BGC BGC 0.4 0.673469
210 MAN BMA BMA 0.4 0.673469
211 MLR 0.4 0.673469
212 DXI 0.4 0.673469
213 GLC BGC BGC BGC BGC BGC 0.4 0.673469
214 BMA BMA BMA 0.4 0.673469
215 CTT 0.4 0.673469
216 CTR 0.4 0.673469
217 SIA GAL SIA GLC NGA 0.4 0.924528
218 GLC BGC GLC 0.4 0.673469
219 BGC BGC BGC BGC BGC BGC 0.4 0.673469
220 GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.673469
221 GLC GLC GLC GLC GLC 0.4 0.673469
222 BGC GLC GLC GLC 0.4 0.673469
223 CE5 0.4 0.673469
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F7Y; Ligand: GLC GAL NAG GAL FUC A2G; Similar sites found: 58
This union binding pocket(no: 1) in the query (biounit: 5f7y.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FE2 AIR 0.00684 0.41136 2.7451
2 4DSU BZI 0.0008167 0.40722 3.1746
3 4UUG PXG 0.012 0.4123 3.31325
4 2VDF OCT 0.00004122 0.5422 3.33333
5 3MJE NDP 0.02543 0.4017 3.33333
6 4HXY NDP 0.01481 0.41579 3.88128
7 2GQS C2R 0.008519 0.40495 4.21941
8 2AG4 LP3 0.04686 0.41231 5.4878
9 2AG4 OLA 0.04629 0.40947 5.4878
10 3A7R LAQ 0.008072 0.43358 5.83333
11 1PKX XMP 0.01702 0.40189 5.83333
12 4XMF HSM 0.008362 0.41411 5.97826
13 5LYH 7B8 0.004991 0.43925 6.21762
14 2HJR APR 0.02143 0.40005 7.29614
15 4TWP AXI 0.04047 0.41695 7.38007
16 4WHZ 3NL 0.03206 0.41219 7.5
17 5BVE 4VG 0.04677 0.41114 7.5
18 5W4W 9WG 0.02126 0.40679 7.5
19 4KBA 1QM 0.013 0.40242 7.5
20 2OFW ADX 0.02707 0.40903 7.69231
21 2QHV OC9 0.002779 0.43484 8.33333
22 2QHS OCA 0.002826 0.42943 8.33333
23 4TXJ THM 0.02247 0.40559 8.33333
24 5T8U LPA 0.009485 0.40054 8.33333
25 4I54 1C1 0.02252 0.40554 8.49858
26 3WYJ H78 0.03086 0.42332 9.16667
27 2E5A LAQ 0.0126 0.41549 9.16667
28 4OYA 1VE 0.01673 0.43699 9.22747
29 1VJY 460 0.03018 0.40035 9.24092
30 1KGI T4A 0.007863 0.41964 9.44882
31 1V3S ATP 0.007465 0.41562 9.48276
32 5DEP UD1 0.03197 0.40021 9.68992
33 1JG3 ADN 0.02394 0.40301 9.78723
34 4CE5 PDG 0.0138 0.41081 10
35 5DQ8 FLF 0.02303 0.40506 10.4167
36 4XSH NAI 0.01622 0.40446 10.6145
37 5IXG OTP 0.03502 0.40939 10.6509
38 1R2Q GNP 0.02232 0.40916 10.8333
39 3A5Z KAA 0.01569 0.40808 11.5183
40 3TAY MN0 0.01523 0.40728 12.5
41 4K38 SAM 0.01284 0.40263 12.5
42 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.00989 0.40407 13.3333
43 5JFL NAD 0.02506 0.40202 13.3333
44 4LY9 S6P 0.01254 0.43257 14.1667
45 4LY9 1YY 0.01302 0.43257 14.1667
46 1OX5 1PR 0.02277 0.40283 14.1667
47 4PAB THG 0.005613 0.41553 15
48 1ORR NAD 0.02026 0.41129 15
49 5MX4 HPA 0.005183 0.42788 15.4506
50 5A89 ADP 0.0085 0.43856 15.8333
51 5A89 FMN 0.0085 0.43856 15.8333
52 1TU3 GNP 0.01642 0.4085 17.7215
53 1Z0J GTP 0.01759 0.40566 18.3333
54 1O44 852 0.03181 0.40544 19.4444
55 2G30 ALA ALA PHE 0.0000606 0.51566 20.8333
56 2J9D ADP 0.00843 0.41488 27.5
57 2J9D AMP 0.01226 0.4017 27.5
58 3TMK T5A 0.007292 0.42715 31.4815
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