Receptor
PDB id Resolution Class Description Source Keywords
5FQH 2.1 Å EC: 7.-.-.- THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURA OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRI CLOSTRIDIUM PERFRINGENS BETA-N-ACETYLGALACTOSAMINIDASE GLYCOSIDE HYDROLASE GH123 GLYCOSPHINGOLIPID GANGLIOSIDE GLOBOSIDE SUBSTRATE- ASSISCATALYSIS HYDROLASE
Ref.: THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDRO FROM CLOSTRIDIUM PERFRINGENS J.MOL.BIOL. V. 428 3253 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:1589;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
NGA GAL BGC A:1586;
Valid;
none;
submit data
545.491 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FR0 1.75 Å EC: 7.-.-.- THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDROLASE F ROM CLOSTRIDIUM PERFRINGENS CLOSTRIDIUM PERFRINGENS HYDROLASE GLYCOSIDE HYDROLASE GH123 GLYCOSPHINGOLIPID GANGLIOSIDE GLOBOSIDE SUBSTRATE-ASSISTED CATALYSIS.
Ref.: THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDRO FROM CLOSTRIDIUM PERFRINGENS J.MOL.BIOL. V. 428 3253 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
2 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
3 5FQG - NGA GAL n/a n/a
4 5FQH - NGA GAL BGC n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
2 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
3 5FQG - NGA GAL n/a n/a
4 5FQH - NGA 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 181 families.
1 5L7U - NGA C8 H15 N O6 CC(=O)N[C@....
2 5L7V Kd = 9.6 nM GNL C8 H13 N O4 S CC1=N[C@@H....
3 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
4 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
5 5FQG - NGA GAL n/a n/a
6 5FQH - NGA GAL BGC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NGA GAL BGC; Similar ligands found: 341
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA GAL BGC 1 1
2 NGA GLA GAL BGC 0.842857 1
3 NAG GAL BGC 0.771429 1
4 MBG A2G 0.701493 0.957447
5 A2G MBG 0.701493 0.957447
6 GAL NGA GLA BGC GAL 0.666667 1
7 GLC GAL NAG GAL 0.662338 1
8 NAG GDL 0.661765 0.9375
9 CBS CBS 0.661765 0.9375
10 CBS 0.661765 0.9375
11 NAG NDG 0.661765 0.9375
12 A2G GAL BGC FUC 0.658537 0.978261
13 BMA BMA BMA BMA BMA BMA 0.650794 0.733333
14 MLR 0.650794 0.733333
15 BMA MAN BMA 0.650794 0.733333
16 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.650794 0.733333
17 GAL GAL GAL 0.650794 0.733333
18 MAN BMA BMA 0.650794 0.733333
19 BGC BGC BGC GLC 0.650794 0.733333
20 BGC GLC GLC GLC 0.650794 0.733333
21 BMA BMA BMA 0.650794 0.733333
22 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.650794 0.733333
23 CE8 0.650794 0.733333
24 GLC BGC BGC 0.650794 0.733333
25 CE6 0.650794 0.733333
26 GLC GLC GLC GLC GLC GLC GLC GLC 0.650794 0.733333
27 GLA GAL GLC 0.650794 0.733333
28 MT7 0.650794 0.733333
29 BGC GLC GLC 0.650794 0.733333
30 BGC BGC BGC BGC BGC BGC 0.650794 0.733333
31 MTT 0.650794 0.733333
32 BGC GLC GLC GLC GLC GLC GLC 0.650794 0.733333
33 CE5 0.650794 0.733333
34 GLC GLC GLC GLC GLC 0.650794 0.733333
35 GLC BGC BGC BGC BGC BGC 0.650794 0.733333
36 CT3 0.650794 0.733333
37 GLC BGC BGC BGC BGC 0.650794 0.733333
38 GLC GLC BGC 0.650794 0.733333
39 DXI 0.650794 0.733333
40 MAN MAN BMA BMA BMA BMA 0.650794 0.733333
41 B4G 0.650794 0.733333
42 BGC GLC GLC GLC GLC 0.650794 0.733333
43 BMA BMA BMA BMA BMA 0.650794 0.733333
44 CEX 0.650794 0.733333
45 GLC GLC GLC GLC GLC GLC GLC 0.650794 0.733333
46 CTT 0.650794 0.733333
47 GLC GAL GAL 0.650794 0.733333
48 MAN BMA BMA BMA BMA 0.650794 0.733333
49 CTR 0.650794 0.733333
50 GLC GLC BGC GLC GLC GLC GLC 0.650794 0.733333
51 GLC BGC GLC 0.650794 0.733333
52 CEY 0.650794 0.733333
53 NAG NAG NAG NAG NAG NAG 0.647887 0.918367
54 CTO 0.647887 0.918367
55 NDG NAG NAG NDG NAG 0.647887 0.918367
56 NAG NAG NAG NAG NAG 0.647887 0.918367
57 NAG NAG NAG NAG NDG NAG 0.647887 0.918367
58 NAG NAG NAG NAG NDG 0.647887 0.918367
59 NDG NAG NAG NDG 0.647887 0.918367
60 NAG NAG NDG 0.647887 0.918367
61 NDG NAG NAG 0.647887 0.918367
62 NDG NAG NAG NAG 0.647887 0.918367
63 NAG NAG NAG 0.647887 0.918367
64 NAG NAG NAG NDG 0.647887 0.918367
65 NAG NAG NAG NAG NAG NAG NAG NAG 0.647887 0.918367
66 NAG NAG NAG NAG 0.647887 0.918367
67 NAG GAL 0.623188 1
68 NGA GAL 0.623188 1
69 GAL NAG 0.623188 1
70 LAT NAG GAL 0.615385 1
71 BGC GAL NAG GAL 0.615385 1
72 GAL NAG GAL BGC 0.615385 1
73 BMA BMA BMA BMA BMA BMA MAN 0.61194 0.717391
74 MAN BMA BMA BMA BMA BMA 0.61194 0.717391
75 MAN NAG 0.608696 1
76 NAG GAL NAG 0.589744 0.9375
77 GAL GLC 0.587302 0.733333
78 MAL 0.587302 0.733333
79 MAB 0.587302 0.733333
80 BGC GLC 0.587302 0.733333
81 N9S 0.587302 0.733333
82 BGC BMA 0.587302 0.733333
83 GLC BGC 0.587302 0.733333
84 GLA GLA 0.587302 0.733333
85 BMA GAL 0.587302 0.733333
86 CBI 0.587302 0.733333
87 B2G 0.587302 0.733333
88 CBK 0.587302 0.733333
89 GLC GAL 0.587302 0.733333
90 GAL BGC 0.587302 0.733333
91 MAL MAL 0.587302 0.717391
92 LAT 0.587302 0.733333
93 LBT 0.587302 0.733333
94 BGC GAL 0.587302 0.733333
95 GLA GAL 0.587302 0.733333
96 BMA BMA 0.587302 0.733333
97 A2G GAL NAG FUC GAL GLC 0.585106 0.918367
98 GLC GAL NAG GAL FUC A2G 0.585106 0.918367
99 MAN NAG GAL 0.571429 1
100 GAL NAG MAN 0.571429 1
101 BGC BGC BGC BGC 0.569444 0.733333
102 NAG A2G 0.569444 0.9375
103 NAG NGA 0.569444 0.9375
104 BGC BGC BGC BGC BGC BGC BGC BGC 0.569444 0.733333
105 NAG MAN BMA 0.5625 1
106 NAG MAN MAN 0.5625 1
107 NAG NAG 0.56 0.846154
108 NDG GAL 0.549296 1
109 GAL NDG 0.549296 1
110 NLC 0.549296 1
111 NAG GAL GAL NAG GAL 0.548781 0.9375
112 FUC BGC GAL NAG 0.54023 0.978261
113 GLC GLC GLC BGC 0.539474 0.733333
114 FUC GLA A2G 0.5375 0.978261
115 A2G GAL FUC 0.5375 0.978261
116 NGA GAL FUC 0.5375 0.978261
117 FUC GAL A2G 0.5375 0.978261
118 A2G GLA FUC 0.5375 0.978261
119 FUC GL0 A2G 0.5375 0.978261
120 ABD 0.535714 0.977778
121 NAG NAG NAG NAG NAG NAG NAG 0.534884 0.833333
122 BGC FUC GAL FUC A2G 0.534091 0.957447
123 GLC FUC GAL FUC A2G 0.534091 0.957447
124 NDG NAG 0.533333 0.918367
125 BMA BMA GLA BMA BMA 0.532468 0.733333
126 NAG NGO 0.531646 0.865385
127 GAL NAG GAL NAG GAL NAG 0.53012 0.918367
128 DLD 0.53012 0.775862
129 NAG GAL GAL NAG 0.53012 0.9375
130 FUC GAL NAG GAL BGC 0.527473 0.978261
131 NAG MBG 0.527027 0.957447
132 GAL BGC NAG GAL 0.52439 1
133 NOJ NAG NAG 0.52381 0.833333
134 NOJ NAG NAG NAG 0.52381 0.818182
135 SIA GAL BGC NGA 0.52381 0.865385
136 BGC GAL SIA NGA 0.52381 0.865385
137 GAL BGC SIA NGA 0.52381 0.865385
138 SN5 SN5 0.52 0.803922
139 NAG AMU 0.518072 0.9
140 NAG NDG BMA 0.518072 0.865385
141 NAG NAG BMA 0.518072 0.865385
142 NAG MUB 0.518072 0.9
143 GLA GAL GAL 0.513889 0.733333
144 GLA GAL BGC 0.513889 0.733333
145 A2G GAL NAG FUC 0.511111 0.918367
146 GAL NAG GAL 0.506024 0.957447
147 NGT NAG 0.506024 0.775862
148 LAT GLA 0.5 0.733333
149 NAG MAN MAN MAN NAG 0.5 0.9375
150 NAG NAG BMA MAN NAG 0.5 0.849057
151 BGC BGC GLC 0.5 0.733333
152 NAG GCU NAG GCU NAG GCU 5AX 0.5 0.9
153 NAG BMA NAG MAN MAN NAG NAG 0.5 0.918367
154 GLA GAL NAG FUC GAL GLC 0.5 0.978261
155 NAG BDP NAG BDP NAG BDP NAG 0.5 0.9
156 NAG MAN BMA NDG MAN NAG GAL 0.49505 0.918367
157 MAN MAN NAG 0.493976 0.957447
158 FUC GAL GLC 0.493506 0.755556
159 GLC GAL FUC 0.493506 0.755556
160 LAT FUC 0.493506 0.755556
161 FUC LAT 0.493506 0.755556
162 BGC GAL FUC 0.493506 0.755556
163 MAG 0.492537 0.893617
164 2F8 0.492537 0.893617
165 GLC GAL NAG GAL FUC FUC 0.489583 0.957447
166 BGC GAL NAG GAL FUC FUC 0.489583 0.957447
167 NAG MAN GAL MAN MAN NAG GAL 0.489362 0.9375
168 FUC BGC GAL NAG GAL 0.489362 0.978261
169 NAG AMU NAG AMV 0.488889 0.882353
170 NAG NAG NGT 0.488636 0.762712
171 6Y2 0.488636 0.703125
172 TCG 0.488095 0.775862
173 CTO TMX 0.488095 0.775862
174 NAG MAN MMA 0.487805 0.957447
175 NAG GAL GAL 0.4875 1
176 MAN BMA NAG 0.4875 1
177 GLA GAL NAG 0.4875 1
178 8VZ 0.486486 0.918367
179 ARE 0.484211 0.836735
180 AAO 0.484211 0.836735
181 3QL 0.481481 0.865385
182 GUM 0.478723 0.803571
183 TXT 0.477273 0.87234
184 GAC 0.477273 0.87234
185 NAG NM9 0.47619 0.882353
186 BGC BGC XYS BGC 0.47619 0.702128
187 M5G 0.475728 0.9375
188 GLC GLC GLC GLC GLC GLC 0.474359 0.733333
189 NAG NAG BMA MAN MAN 0.473684 0.9375
190 MAN MAN NAG MAN NAG 0.473684 0.9375
191 AO3 0.473118 0.692308
192 XYS BGC BGC BGC BGC XYS BGC BGC BGC 0.471264 0.702128
193 XYS BGC BGC XYS BGC XYS BGC BGC BGC 0.471264 0.702128
194 BGC BGC BGC XYS BGC BGC 0.471264 0.702128
195 G6S NAG 0.46988 0.762712
196 UMG 0.46875 0.803571
197 FUC GAL NAG A2G FUC 0.468085 0.918367
198 NAG GAL FUC FUC A2G 0.468085 0.918367
199 NAG NAG BMA MAN 0.467391 0.865385
200 GAL A2G 0.466667 1
201 GAL NGA 0.466667 1
202 A2G GAL 0.466667 1
203 AH0 NAG 0.465116 0.833333
204 NG1 0.464789 0.75
205 GN1 0.464789 0.75
206 GAL NGA A2G 0.4625 0.918367
207 SIA GAL SIA GLC NGA 0.462185 0.849057
208 SIA GAL SIA BGC NGA 0.462185 0.849057
209 QPS 0.461538 0.836735
210 ACR 0.461538 0.836735
211 GAL GAL GLC EMB MEC 0.458333 0.75
212 GLA EGA 0.458333 0.73913
213 NAA NAA AMI 0.458333 0.661765
214 DR5 0.457143 0.73913
215 MMA MAN 0.457143 0.73913
216 NDG BDP BDP NPO NDG 0.456311 0.703125
217 GLC GLC XYP 0.455696 0.733333
218 NAG FUC 0.454545 0.934783
219 GLC GLC DAF BGC 0.453608 0.8
220 GLC GLC AGL HMC GLC 0.453608 0.8
221 ACR GLC GLC GLC 0.453608 0.8
222 GLC GLC ACI G6D GLC GLC 0.453608 0.8
223 3YW 0.453333 0.913043
224 FUL GAL NAG 0.452381 0.978261
225 DR2 0.452381 0.978261
226 NDG GAL FUC 0.452381 0.978261
227 FUC GAL NAG 0.452381 0.978261
228 FUC GAL NDG 0.452381 0.978261
229 ACG 0.44898 0.8
230 NAG BMA 0.448718 0.897959
231 GLC GLC BGC XYS BGC XYS 0.448276 0.702128
232 GLA GAL BGC 5VQ 0.447368 0.708333
233 BGC GLA GAL FUC 0.447059 0.755556
234 NAG MAN GAL BMA NAG MAN NAG GAL 0.445545 0.918367
235 MAN BMA NAG NAG MAN NAG GAL GAL 0.445545 0.918367
236 NAG MAN GAL BMA NDG MAN NAG GAL 0.445545 0.918367
237 NAG MAN MAN MAN NAG GAL NAG GAL 0.445545 0.918367
238 ACI GLD GLC GAL 0.444444 0.851064
239 DAF BGC GLC 0.444444 0.851064
240 DAF GLC GLC 0.444444 0.851064
241 GLC GLC G6D ACI GLC GLC GLC 0.442105 0.851064
242 QV4 0.442105 0.836735
243 BGA 0.442105 0.818182
244 NAG AH0 0.43956 0.833333
245 NAG NAG BMA MAN MAN NAG NAG 0.439252 0.849057
246 BGC BGC BGC XYS GAL 0.438202 0.702128
247 MA8 0.4375 0.843137
248 SIA GAL NGA 0.436893 0.865385
249 4U0 0.436893 0.9
250 GYU 0.435897 0.767857
251 GLC GLC FRU 0.435294 0.66
252 GLC GLC GLC G6D ADH GLC 0.434343 0.754717
253 GLA GAL GLC NBU 0.43038 0.68
254 G2F BGC BGC BGC BGC BGC 0.43038 0.66
255 7SA 0.43 0.803922
256 NAG GDL PHJ 0.43 0.737705
257 GAL NAG GAL FUC 0.428571 0.978261
258 GLA NAG GAL FUC 0.428571 0.978261
259 GAL MGC 0.428571 0.957447
260 SIA GAL NAG GAL GLC 0.42735 0.849057
261 BGC GAL NAG SIA GAL 0.42735 0.849057
262 SIA GAL NAG GAL BGC 0.42735 0.849057
263 BGC BGC XYS BGC XYS BGC XYS 0.426966 0.702128
264 BGC BGC BGC XYS BGC XYS XYS 0.426966 0.702128
265 GLC BGC BGC XYS BGC XYS XYS 0.426966 0.702128
266 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.425926 0.9375
267 MMA MAN NAG MAN NAG NAG 0.425532 0.9
268 GAL FUC 0.424658 0.733333
269 G6D GLC ACI GLD GLC ACI GLD GLC BGC 0.424242 0.75
270 NAG NAG BMA BMA 0.423913 0.833333
271 LEC NGA 0.423913 0.703125
272 GAL NAG FUC 0.423529 0.978261
273 GAL NDG FUC 0.423529 0.978261
274 FUC NAG GAL 0.423529 0.978261
275 FUC NDG GAL 0.423529 0.978261
276 GAL NGA SIA GAL BGC 0.422414 0.865385
277 SIA GAL BGC NGA GAL 0.422414 0.865385
278 BGC GAL SIA NGA GAL 0.422414 0.865385
279 GAL NGA GAL BGC SIA 0.422414 0.865385
280 SLT 0.421569 0.918367
281 3PV 0.421053 0.9
282 G3I 0.419753 0.76
283 G2I 0.419753 0.76
284 ACR GLC 0.419355 0.8
285 ACR GLC GLC GLC GLC 0.419355 0.8
286 NAG GCU NAG GCD 0.419048 0.833333
287 DEL 0.418919 0.717391
288 WZ5 0.418367 0.957447
289 BM3 0.41791 0.888889
290 A2G 0.41791 0.888889
291 HSQ 0.41791 0.888889
292 NGA 0.41791 0.888889
293 NAG 0.41791 0.888889
294 NDG 0.41791 0.888889
295 TNR 0.417722 0.86
296 SIA BGC GAL 0.413462 0.9
297 SIA GAL GLC 0.413462 0.9
298 BGC GAL SIA 0.413462 0.9
299 GAL BGC SIA 0.413462 0.9
300 BGC SIA GAL 0.413462 0.9
301 GLA GLC SIA 0.413462 0.9
302 SIA GAL BGC 0.413462 0.9
303 MAL EDO 0.413333 0.702128
304 FUC BGC GAL 0.4125 0.755556
305 DAF GLC DAF GLC GLC 0.412371 0.816327
306 AC1 GLC AC1 BGC 0.412371 0.816327
307 GLC ACI GLD GAL 0.412371 0.8
308 ACI GLD GLC GLC GLC ACI GLD GLC GAL 0.412371 0.816327
309 ACI G6D GLC ACI G6D BGC 0.412371 0.816327
310 GLC ACI G6D GLC 0.412371 0.8
311 ACI GLD GLC ACI G6D BGC 0.412371 0.816327
312 BGC GLC AC1 GLC GLC GLC AC1 0.412371 0.816327
313 FUC GAL NAG GAL FUC 0.410526 0.957447
314 NAG BMA MAN MAN MAN MAN 0.410526 1
315 GLC GLC XYS 0.409639 0.755556
316 GAL NGA GAL SIA 0.409091 0.865385
317 SIA GAL NGA GAL 0.409091 0.865385
318 3SA 0.406593 0.836735
319 BGC BGC BGC XYS BGC XYS GAL 0.40625 0.702128
320 GAL BGC BGC BGC XYS BGC XYS 0.40625 0.702128
321 NAG MU2 0.40566 0.818182
322 U63 0.405405 0.673469
323 BDZ 0.404494 0.957447
324 FUC GAL NAG FUC 0.404494 0.957447
325 GAL NAG FUC FUC 0.404494 0.957447
326 FUC NAG GAL FUC 0.404494 0.957447
327 BCW 0.404494 0.957447
328 FUC NDG GAL FUC 0.404494 0.957447
329 FUC GAL NDG FUC 0.404494 0.957447
330 SN5 NGT 0.404494 0.694915
331 GAL NDG FUC FUC 0.404494 0.957447
332 GLC BGC BGC BGC XYS BGC XYS XYS 0.404255 0.6875
333 GLC AGL GLC HMC 0.40404 0.784314
334 NOK GAL 0.402439 0.814815
335 OXZ BGC BGC 0.402439 0.690909
336 GAL NOK 0.402439 0.814815
337 UNU GAL NAG 0.402174 0.918367
338 GLC ACI G6D BGC 0.4 0.851064
339 GLC G6D ACI GLC 0.4 0.851064
340 GLC G6D ADH GLC 0.4 0.851064
341 GLC ACI GLD GLC 0.4 0.851064
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FR0; Ligand: SIZ; Similar sites found: 4
This union binding pocket(no: 1) in the query (biounit: 5fr0.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YKD CMP 0.01042 0.40502 2.26131
2 4ZW3 4S9 0.02799 0.40528 2.29508
3 2PWG CTS 0.01303 0.40233 3.77698
4 4J25 OGA 0.01276 0.40847 10.0437
Feedback