Receptor
PDB id Resolution Class Description Source Keywords
1C4Q 1.52 Å NON-ENZYME: TOXIN_VIRAL MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE ESCHERICHIA COLI TOXIN RECEPTOR BINDING PROTEIN-CARBOHYDRATE RECOGNITION OB-FOLD
Ref.: IDENTIFICATION OF THE PRIMARY RECEPTOR BINDING SITE OF SHIGA-LIKE TOXIN B SUBUNITS: STRUCTURES OF MUTATED SHIGA-LIKE TOXIN I B-PENTAMER WITH AND WITHOUT BOUND CARBOHYDRATE TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLA GAL BGC A:190;
B:290;
C:390;
D:490;
E:590;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
504.438 n/a O(C1O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1C4Q 1.52 Å NON-ENZYME: TOXIN_VIRAL MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE ESCHERICHIA COLI TOXIN RECEPTOR BINDING PROTEIN-CARBOHYDRATE RECOGNITION OB-FOLD
Ref.: IDENTIFICATION OF THE PRIMARY RECEPTOR BINDING SITE OF SHIGA-LIKE TOXIN B SUBUNITS: STRUCTURES OF MUTATED SHIGA-LIKE TOXIN I B-PENTAMER WITH AND WITHOUT BOUND CARBOHYDRATE TO BE PUBLISHED
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 1QNU - GAL GAL GLC EMB MEC n/a n/a
2 1CQF - GLA GAL BGC n/a n/a
3 1D1I - GLA GAL BGC n/a n/a
4 1D1K - GLA GAL GLC n/a n/a
5 1C4Q - GLA GAL BGC n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 2BOS - GLA GAL GLC n/a n/a
2 1QNU - GAL GAL GLC EMB MEC n/a n/a
3 1CQF - GLA GAL BGC n/a n/a
4 1D1I - GLA GAL BGC n/a n/a
5 1D1K - GLA GAL GLC n/a n/a
6 1C4Q - GLA GAL BGC n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 2BOS - GLA GAL GLC n/a n/a
2 1QNU - GAL GAL GLC EMB MEC n/a n/a
3 1CQF - GLA GAL BGC n/a n/a
4 1D1I - GLA GAL BGC n/a n/a
5 1D1K - GLA GAL GLC n/a n/a
6 1C4Q - GLA GAL BGC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLA GAL BGC; Similar ligands found: 298
No: Ligand ECFP6 Tc MDL keys Tc
1 GLA GAL GAL 1 1
2 GLA GAL BGC 1 1
3 BGC BGC BGC BGC 0.924528 1
4 BGC BGC BGC BGC BGC BGC BGC BGC 0.924528 1
5 MAL MAL 0.816327 0.970588
6 BGC BMA 0.816327 1
7 B2G 0.816327 1
8 N9S 0.816327 1
9 GLA GAL 0.816327 1
10 GLC BGC 0.816327 1
11 GLC GAL 0.816327 1
12 MAB 0.816327 1
13 BGC GAL 0.816327 1
14 CBK 0.816327 1
15 GAL BGC 0.816327 1
16 GLA GLA 0.816327 1
17 CBI 0.816327 1
18 GAL GLC 0.816327 1
19 BMA BMA 0.816327 1
20 BMA GAL 0.816327 1
21 LAT 0.816327 1
22 BGC GLC 0.816327 1
23 LBT 0.816327 1
24 MAL 0.816327 1
25 CTR 0.754717 1
26 BGC GLC GLC GLC GLC GLC GLC 0.754717 1
27 CEY 0.754717 1
28 CE8 0.754717 1
29 GLA GAL GLC 0.754717 1
30 GAL GAL GAL 0.754717 1
31 GLC GLC GLC GLC GLC 0.754717 1
32 MAN BMA BMA 0.754717 1
33 MTT 0.754717 1
34 GLC GLC GLC GLC GLC GLC GLC GLC 0.754717 1
35 BMA BMA BMA BMA BMA BMA 0.754717 1
36 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.754717 1
37 BGC GLC GLC 0.754717 1
38 GLC BGC BGC BGC BGC 0.754717 1
39 MT7 0.754717 1
40 MLR 0.754717 1
41 GLC BGC BGC 0.754717 1
42 BMA BMA BMA 0.754717 1
43 BGC BGC BGC BGC BGC BGC 0.754717 1
44 BGC BGC BGC GLC 0.754717 1
45 B4G 0.754717 1
46 CEX 0.754717 1
47 CE6 0.754717 1
48 GLC GLC BGC 0.754717 1
49 CT3 0.754717 1
50 CE5 0.754717 1
51 BMA BMA BMA BMA BMA 0.754717 1
52 BGC GLC GLC GLC GLC 0.754717 1
53 GLC GLC GLC GLC GLC GLC GLC 0.754717 1
54 GLC GLC BGC GLC GLC GLC GLC 0.754717 1
55 MAN MAN BMA BMA BMA BMA 0.754717 1
56 BMA MAN BMA 0.754717 1
57 GLC BGC BGC BGC BGC BGC 0.754717 1
58 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.754717 1
59 BGC GLC GLC GLC 0.754717 1
60 CTT 0.754717 1
61 MAN BMA BMA BMA BMA 0.754717 1
62 GLC GAL GAL 0.754717 1
63 DXI 0.754717 1
64 GLC BGC GLC 0.754717 1
65 GAL NAG GAL BGC 0.716418 0.733333
66 BGC GAL NAG GAL 0.716418 0.733333
67 LAT NAG GAL 0.716418 0.733333
68 GLC BGC BGC BGC BGC BGC BGC 0.709091 1
69 BGC BGC BGC 0.709091 1
70 BGC BGC BGC ASO BGC BGC ASO 0.709091 1
71 BGC BGC BGC BGC BGC 0.709091 1
72 GLC BGC BGC BGC 0.709091 1
73 BGC BGC BGC GLC BGC BGC 0.709091 1
74 MAN BMA BMA BMA BMA BMA 0.701754 0.970588
75 BMA BMA BMA BMA BMA BMA MAN 0.701754 0.970588
76 GLC GAL NAG GAL 0.695652 0.733333
77 GAL NGA GLA BGC GAL 0.676056 0.733333
78 BGC BGC GLC 0.672414 1
79 NAG GAL BGC 0.661765 0.733333
80 NGA GLA GAL BGC 0.638889 0.733333
81 MAN BMA NAG 0.636364 0.733333
82 NAG GAL GAL 0.636364 0.733333
83 GLA GAL NAG 0.636364 0.733333
84 MAN GLC 0.618182 1
85 M3M 0.618182 1
86 LB2 0.618182 1
87 SGA BGC 0.616667 0.702128
88 MAN MAN MAN GLC 0.609375 1
89 BMA BMA GLA BMA BMA 0.597015 1
90 5GO 0.596774 0.66
91 M13 0.596491 0.942857
92 GAL MBG 0.596491 0.942857
93 MDM 0.596491 0.942857
94 GLC GLC GLC BGC 0.58209 1
95 BGC GLA GAL FUC 0.577465 0.970588
96 LAT GLA 0.571429 1
97 GLA GAL NAG FUC GAL GLC 0.564706 0.717391
98 FUC GAL NAG GAL BGC 0.560976 0.717391
99 P3M 0.552239 0.767442
100 U63 0.55 0.891892
101 BMA BMA MAN 0.55 0.970588
102 NAG GAL GAL NAG GAL 0.546667 0.6875
103 NAG GAL GAL NAG 0.546667 0.6875
104 GAL NAG GAL NAG GAL NAG 0.546667 0.673469
105 BGC BGC 0.54386 1
106 MAN MAN 0.54386 1
107 2M4 0.54386 1
108 MMA MAN 0.542373 0.942857
109 DR5 0.542373 0.942857
110 GLA EGA 0.540984 0.942857
111 BGC GAL NAG GAL FUC FUC 0.534884 0.702128
112 GLC GAL NAG GAL FUC FUC 0.534884 0.702128
113 GLC GLC BGC XYS BGC XYS 0.533333 0.942857
114 BMA MAN MAN 0.53125 1
115 LAT FUC 0.529412 0.970588
116 FUC GAL GLC 0.529412 0.970588
117 GLC GAL FUC 0.529412 0.970588
118 GLC GLC GLC GLC GLC GLC 0.529412 1
119 BGC GAL FUC 0.529412 0.970588
120 FUC LAT 0.529412 0.970588
121 GAL FUC 0.52459 0.941176
122 MAN MAN BMA MAN 0.521739 1
123 MAN MAN MAN MAN 0.521739 1
124 XYS BGC BGC XYS BGC XYS BGC BGC BGC 0.519481 0.942857
125 BGC BGC BGC XYS GAL 0.519481 0.942857
126 XYS BGC BGC BGC BGC XYS BGC BGC BGC 0.519481 0.942857
127 BGC BGC BGC XYS BGC BGC 0.519481 0.942857
128 NGA GAL BGC 0.513889 0.733333
129 ABD 0.512821 0.75
130 BMA MAN 0.508197 0.914286
131 MAL EDO 0.507937 0.942857
132 GAL GAL SO4 0.507463 0.702128
133 GLC GAL NAG GAL FUC A2G 0.5 0.673469
134 GAL NDG 0.5 0.733333
135 A2G GAL NAG FUC GAL GLC 0.5 0.673469
136 NLC 0.5 0.733333
137 NDG GAL 0.5 0.733333
138 GLC GLC FRU 0.5 0.868421
139 GAL BGC BGC XYS 0.5 0.942857
140 MAN MAN MAN BMA MAN 0.493333 1
141 MAN BMA MAN MAN MAN 0.492958 1
142 M5S 0.492958 1
143 MVP 0.492308 0.733333
144 DEL 0.492063 0.970588
145 GLC G6D ACI GLC 0.487805 0.785714
146 GLC ACI G6D BGC 0.487805 0.785714
147 GLC ACI GLD GLC 0.487805 0.785714
148 GLC G6D ADH GLC 0.487805 0.785714
149 BGC BGC XYS BGC 0.486842 0.942857
150 NAG GAL NAG 0.486842 0.6875
151 GLC GLC XYP 0.485714 1
152 MAN MAN BMA 0.484375 1
153 FUC BGC GAL NAG GAL 0.482759 0.717391
154 NAG BMA MAN MAN MAN MAN 0.481928 0.733333
155 TRE 0.480769 1
156 G2F BGC BGC BGC BGC BGC 0.478261 0.868421
157 GLA GAL BGC 5VQ 0.477612 0.891892
158 NAG NAG BMA MAN 0.47619 0.634615
159 BGC BGC BGC XYS BGC XYS GAL 0.47619 0.942857
160 GAL BGC BGC BGC XYS BGC XYS 0.47619 0.942857
161 CGC 0.469697 0.941176
162 BGC BGC XYS BGC XYS BGC XYS 0.468354 0.942857
163 BGC BGC BGC XYS BGC XYS XYS 0.468354 0.942857
164 GLC BGC BGC XYS BGC XYS XYS 0.468354 0.942857
165 GLA MBG 0.466667 0.942857
166 GAL GAL GLC EMB MEC 0.465909 0.622642
167 GLC ACI GLD GAL 0.465116 0.733333
168 GLC GLC G6D ACI GLC GLC GLC 0.465116 0.785714
169 GLC ACI G6D GLC 0.465116 0.733333
170 GLC BGC BGC BGC XYS BGC XYS XYS 0.457831 0.916667
171 GLA GAL GLC NBU 0.457143 0.846154
172 MAN MMA MAN 0.457143 0.942857
173 FUC BGC GAL 0.457143 0.970588
174 GLC GLC GLC GLC 0.457143 1
175 4MU MAN MAN 0.45679 0.767442
176 BGC BGC ZZ1 0.45679 0.767442
177 GAL XYS XYS BGC BGC BGC XYS GAL BGC 0.454545 0.942857
178 GLC BGC BGC XYS BGC XYS XYS GAL 0.454545 0.942857
179 GLC BGC BGC XYS BGC XYS XYS GAL GAL 0.454545 0.942857
180 GLC AGL GLC HMC 0.454545 0.717391
181 GAL BGC BGC BGC XYS XYS 0.454545 0.942857
182 BGC BGC XYS BGC GAL XYS BGC XYS GAL 0.454545 0.942857
183 GLA MAN RAM ABE GLA MAN RAM ABE 0.450549 0.868421
184 GLA MAN RAM TYV GLA MAN RAM TYV 0.450549 0.868421
185 NAG NAG BMA MAN MAN 0.449438 0.6875
186 MAN MAN NAG MAN NAG 0.449438 0.6875
187 GAL NAG MAN 0.447368 0.733333
188 OPM MAN MAN 0.447368 0.804878
189 MAN NAG GAL 0.447368 0.733333
190 DMU 0.444444 0.785714
191 ARE 0.444444 0.733333
192 OXZ BGC BGC 0.444444 0.6875
193 G2I 0.444444 0.767442
194 GLC GLC DAF BGC 0.444444 0.733333
195 UMQ 0.444444 0.785714
196 GLC GLC AGL HMC GLC 0.444444 0.733333
197 GLC GLC ACI G6D GLC GLC 0.444444 0.733333
198 LMU 0.444444 0.785714
199 AAO 0.444444 0.733333
200 G3I 0.444444 0.767442
201 LMT 0.444444 0.785714
202 ACR GLC GLC GLC 0.444444 0.733333
203 GTM BGC BGC 0.44 0.868421
204 GLC GLC GLC G6D ADH GLC 0.43956 0.6875
205 SOR GLC GLC 0.438356 0.970588
206 DOM 0.4375 0.942857
207 A2G GAL BGC FUC 0.436782 0.717391
208 8VZ 0.434783 0.673469
209 GAL A2G 0.434783 0.733333
210 GAL NGA 0.434783 0.733333
211 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.434783 0.733333
212 A2G GAL 0.434783 0.733333
213 FMO 0.432836 0.868421
214 GLC GLC XYS 0.432432 0.970588
215 BGC BGC G2F SHG 0.43038 0.846154
216 FUC BGC GAL NAG 0.430233 0.717391
217 BGC SGC BGC SGC BGC SGC BGC SGC 0.428571 0.916667
218 TM6 0.428571 0.916667
219 SOR GLC GLC GLC 0.426667 0.970588
220 LAG 0.426667 0.6
221 6UZ 0.426667 0.846154
222 BMA NGT MAN MAN 0.425287 0.66
223 GAL BGC NAG GAL 0.425 0.733333
224 DAF BGC 0.425 0.785714
225 DAF GLC 0.425 0.785714
226 NOY BGC 0.424242 0.75
227 5QP 0.424242 0.885714
228 GLO GLC GLC 0.423077 0.942857
229 GLA MAN RAM RAM ABE MAN GLA 0.42268 0.868421
230 FUC GAL GLA 0.422535 0.970588
231 GLA GLA FUC 0.422535 0.970588
232 GLA GAL FUC 0.422535 0.970588
233 GAL GAL FUC 0.422535 0.970588
234 FUC GLA GLA 0.422535 0.970588
235 RZM 0.421875 0.688889
236 NAG MAN GAL BMA NDG MAN NAG GAL 0.421053 0.673469
237 MAN BMA NAG NAG MAN NAG GAL GAL 0.421053 0.673469
238 10M 0.421053 0.733333
239 NAG MAN MAN MAN NAG GAL NAG GAL 0.421053 0.673469
240 NAG MAN GAL BMA NAG MAN NAG GAL 0.421053 0.673469
241 MAN MAN MAN BMA MAN MAN MAN 0.418605 0.942857
242 SIA GAL NAG GAL BGC 0.418182 0.622642
243 SIA GAL NAG GAL GLC 0.418182 0.622642
244 BGC GAL NAG SIA GAL 0.418182 0.622642
245 MAN MNM 0.41791 0.75
246 BGC BGC SGC MGL 0.417722 0.868421
247 MGL SGC GLC GLC 0.417722 0.868421
248 GAC 0.416667 0.767442
249 DAF BGC GLC 0.416667 0.785714
250 ACI GLD GLC GAL 0.416667 0.785714
251 NAG BMA 0.416667 0.653061
252 DAF GLC GLC 0.416667 0.785714
253 TXT 0.416667 0.767442
254 NPJ 0.415584 0.622642
255 WZ3 0.415584 0.916667
256 GAL MGC 0.414286 0.702128
257 GLO GLC GLC GLC 0.4125 0.942857
258 GLC DMJ 0.411765 0.727273
259 NOJ GLC 0.411765 0.727273
260 SLT 0.410526 0.673469
261 M5G 0.41 0.6875
262 3SA 0.409639 0.733333
263 LSE 0.407895 0.6875
264 MLB 0.40625 1
265 GLA BGC 0.40625 1
266 GLA GLC 0.40625 1
267 BGC GLA 0.40625 1
268 GAL GAL 0.40625 1
269 GLA BMA 0.40625 1
270 LAK 0.40625 1
271 BMA GLA 0.40625 1
272 MAN BMA 0.40625 1
273 ABL 0.405797 0.702128
274 RCB 0.405063 0.622642
275 4MU BGC BGC 0.404762 0.767442
276 GLC GLC GLC PO4 SGC GLC 0.404494 0.673469
277 BMA FRU 0.402985 0.842105
278 FRU GAL 0.402985 0.842105
279 ACR 0.402299 0.733333
280 QPS 0.402299 0.733333
281 GAL BGC SIA 0.402062 0.66
282 GLA GLC SIA 0.402062 0.66
283 SIA GAL GLC 0.402062 0.66
284 BGC GAL SIA 0.402062 0.66
285 SIA GAL BGC 0.402062 0.66
286 BGC SIA GAL 0.402062 0.66
287 SIA BGC GAL 0.402062 0.66
288 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.401961 0.6875
289 GAL NGA GAL BGC SIA 0.4 0.634615
290 SIA GAL BGC NGA GAL 0.4 0.634615
291 GAL NAG GAL FUC 0.4 0.717391
292 4MU BGC BGC BGC BGC 0.4 0.767442
293 BGC GAL SIA NGA GAL 0.4 0.634615
294 NAG MAN BMA NDG MAN NAG GAL 0.4 0.673469
295 GLA NAG GAL FUC 0.4 0.717391
296 GAL NGA SIA GAL BGC 0.4 0.634615
297 QV4 0.4 0.733333
298 CM5 0.4 0.891892
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1C4Q; Ligand: GLA GAL BGC; Similar sites found: 1
This union binding pocket(no: 1) in the query (biounit: 1c4q.bio1) has 80 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2P69 PLP 0.002555 0.51161 2.89855
Pocket No.: 2; Query (leader) PDB : 1C4Q; Ligand: GLA GAL BGC; Similar sites found: 21
This union binding pocket(no: 2) in the query (biounit: 1c4q.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Q19 APC 0.003118 0.43546 None
2 5AHW CMP 0.004989 0.42002 None
3 4TM3 FAD 0.0498 0.41482 None
4 3HVJ 705 0.02154 0.41207 None
5 3O7B SAH 0.008129 0.41202 None
6 3AIH BMA MAN MAN 0.01622 0.40773 None
7 3CBG SAH 0.01012 0.40561 None
8 4UZI IMD 0.02804 0.40467 None
9 1K97 CIR 0.03298 0.40464 None
10 1K97 ASP 0.03298 0.40464 None
11 2IV2 MGD 0.02869 0.40676 4.34783
12 5EYP GTP 0.02001 0.40428 7.24638
13 1RSG FAD 0.03062 0.41078 8.69565
14 3C3Y SAH 0.005404 0.42228 14.4928
15 3GD4 FAD 0.03049 0.42113 14.4928
16 3GD4 NAD 0.0426 0.42113 14.4928
17 1JGT APC 0.02001 0.40928 14.4928
18 4XFR CIT 0.01166 0.40489 14.4928
19 1JGT CMA 0.02812 0.40073 14.4928
20 4LNU GTP 0.02255 0.40173 24.6377
21 4CMF PXG 0.01919 0.40092 37.6812
Pocket No.: 3; Query (leader) PDB : 1C4Q; Ligand: GLA GAL BGC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1c4q.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1C4Q; Ligand: GLA GAL BGC; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 1c4q.bio1) has 73 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4TS1 TYR 0.04615 0.4308 None
2 1Y42 TYR 0.04735 0.43014 None
3 5F6U 5VK 0.02235 0.44248 7.24638
4 4YVN EBS 0.04497 0.43306 8.69565
5 2YMZ LAT 0.03786 0.40115 8.69565
6 3WV6 GAL BGC 0.03681 0.4171 14.4928
Pocket No.: 5; Query (leader) PDB : 1C4Q; Ligand: GLA GAL BGC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1c4q.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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