Receptor
PDB id Resolution Class Description Source Keywords
5DL0 2.3 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF GLUCOSIDASE II ALPHA SUBUNIT (GLC1MAN2- FROM) CHAETOMIUM THERMOPHILUM (STRAIN DSM 14144.50 / IMI 039719) ENDOPLASMIC RETICULUM GLYCOSIDE HYDROLASE GLYCOSYLATION H
Ref.: STRUCTURAL BASIS FOR TWO-STEP GLUCOSE TRIMMING BY GLUCOSIDASE II INVOLVED IN ER GLYCOPROTEIN QUALITY SCI REP V. 6 20575 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MAN GLC B:1;
Valid;
none;
submit data
342.297 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DKY 1.6 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF GLUCOSIDASE II ALPHA SUBUNIT (DNJ-BOUND CHAETOMIUM THERMOPHILUM (STRAIN DSM 14144.50 / IMI 039719) ENDOPLASMIC RETICULUM GLYCOSIDE HYDROLASE GLYCOSYLATION H
Ref.: STRUCTURAL BASIS FOR TWO-STEP GLUCOSE TRIMMING BY GLUCOSIDASE II INVOLVED IN ER GLYCOPROTEIN QUALITY SCI REP V. 6 20575 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 5DKZ - GLC GLC n/a n/a
2 5DL0 - MAN GLC n/a n/a
3 5DKY - NOJ C6 H13 N O4 C1[C@@H]([....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5DKZ - GLC GLC n/a n/a
2 5DL0 - MAN GLC n/a n/a
3 5DKY - NOJ C6 H13 N O4 C1[C@@H]([....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 5DKZ - GLC GLC n/a n/a
2 5DL0 - MAN GLC n/a n/a
3 5DKY - NOJ C6 H13 N O4 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MAN GLC; Similar ligands found: 271
No: Ligand ECFP6 Tc MDL keys Tc
1 M3M 1 1
2 LB2 1 1
3 GLA GLA 1 1
4 MAN GLC 1 1
5 GLC BGC 1 1
6 GLC GLC 1 1
7 NGR 1 1
8 GLA GAL 1 1
9 BGC BGC BGC BGC BGC BGC 0.888889 1
10 GLC BGC BGC BGC BGC BGC BGC 0.888889 1
11 BGC BGC BGC GLC BGC BGC 0.888889 1
12 GLC GLC BGC 0.888889 1
13 GLC GLC GLC GLC 0.888889 1
14 GLC GLC GLC 0.888889 1
15 BMA MAN MAN MAN 0.764706 1
16 MAN MAN MAN 0.685185 1
17 MAN BMA MAN 0.685185 1
18 P3M 0.666667 0.767442
19 GAL GAL SO4 0.660714 0.66
20 BQZ 0.644444 0.909091
21 CGC 0.62963 0.941176
22 GLA GAL GAL 0.618182 1
23 MAN BMA MAN MAN MAN 0.616667 1
24 M5S 0.616667 1
25 2M4 0.612245 1
26 BGC GLC 0.612245 1
27 BMA MAN 0.612245 1
28 GAL MBG 0.607843 0.942857
29 M13 0.607843 0.942857
30 MAN MMA 0.607843 0.942857
31 MDM 0.607843 0.942857
32 BGC BGC BGC BGC BGC BGC BGC BGC 0.603448 1
33 GLC GAL 0.6 1
34 BGC BMA 0.6 1
35 N9S 0.6 1
36 CBI 0.6 1
37 GAL BGC 0.6 1
38 BMA BMA 0.6 1
39 LBT 0.6 1
40 BGC GAL 0.6 1
41 CBK 0.6 1
42 LAT 0.6 1
43 B2G 0.6 1
44 MAB 0.6 1
45 MAL 0.6 1
46 BMA GAL 0.6 1
47 MAN BMA BMA 0.584906 1
48 BMA BMA BMA BMA BMA 0.584906 1
49 MTT 0.584906 1
50 CE6 0.584906 1
51 GAL GAL GAL 0.584906 1
52 BMA BMA BMA BMA BMA BMA 0.584906 1
53 B4G 0.584906 1
54 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.584906 1
55 BGC BGC GLC 0.584906 1
56 MLR 0.584906 1
57 BGC BGC BGC GLC 0.584906 1
58 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.584906 1
59 MAN BMA BMA BMA BMA 0.584906 1
60 GLC BGC BGC BGC 0.584906 1
61 GLA GAL BGC 0.584906 1
62 CTT 0.584906 1
63 MAN MAN BMA BMA BMA BMA 0.584906 1
64 BGC GLC GLC 0.584906 1
65 BGC GLC GLC GLC 0.584906 1
66 BMA MAN BMA 0.584906 1
67 BMA BMA BMA 0.584906 1
68 CEY 0.584906 1
69 DXI 0.584906 1
70 CE8 0.584906 1
71 MAN BMA BMA BMA BMA BMA 0.584906 1
72 GLC GAL GAL 0.584906 1
73 BGC GLC GLC GLC GLC 0.584906 1
74 GLC BGC BGC 0.584906 1
75 CE5 0.584906 1
76 GLA GAL GLC 0.584906 1
77 GLC GLC GLC GLC GLC 0.584906 1
78 GLC BGC GLC 0.584906 1
79 CTR 0.584906 1
80 GLC BGC BGC BGC BGC BGC 0.584906 1
81 BGC BGC BGC 0.584906 1
82 CEX 0.584906 1
83 BGC BGC BGC BGC 0.584906 1
84 CT3 0.584906 1
85 BGC GLC GLC GLC GLC GLC GLC 0.584906 1
86 MT7 0.584906 1
87 GLC BGC BGC BGC BGC 0.584906 1
88 TRE 0.581395 1
89 NAG GAL GAL NAG GAL 0.573529 0.6875
90 BMA MAN MAN MAN MAN 0.5625 1
91 GAL FUC 0.555556 0.941176
92 GLA NAG GAL FUC 0.549296 0.717391
93 LAT GLA 0.54902 1
94 MAN MAN MAN GLC 0.540984 1
95 BGC BGC 0.537037 0.914286
96 U63 0.527273 0.891892
97 GAL A2G 0.525424 0.733333
98 GAL NGA 0.525424 0.733333
99 NAG GAL 0.525424 0.733333
100 GAL NAG 0.525424 0.733333
101 FUC BGC GAL 0.52459 0.970588
102 FUC GLC BGC GAL 0.52459 0.970588
103 MAN MAN MAN MAN 0.52381 1
104 MAN MAN BMA MAN 0.52381 1
105 GLA MBG 0.519231 0.942857
106 DR5 0.518519 0.942857
107 MMA MAN 0.518519 0.942857
108 GLA EGA 0.517857 0.942857
109 DOM 0.509091 0.942857
110 BMA BMA MAN 0.508772 1
111 MAN MAN BMA 0.508772 1
112 AAL GAL 0.508475 0.891892
113 47N 0.508475 0.891892
114 GLA GLA FUC 0.508197 0.970588
115 GLA GAL FUC 0.508197 0.970588
116 FUC GAL GLA 0.508197 0.970588
117 GAL GAL FUC 0.508197 0.970588
118 FUC GLA GLA 0.508197 0.970588
119 BGC BGC BGC BGC BGC 0.5 1
120 MAN BMA NAG 0.5 0.733333
121 BGC BGC BGC BGC BGC BGC BGC 0.5 1
122 NOY BGC 0.5 0.702128
123 MAN MAN MAN MAN MAN MAN MAN 0.5 1
124 GAL NGA A2G 0.5 0.6875
125 GLA GAL NAG 0.5 0.733333
126 BMA BMA MAN GLA GLA 0.492063 1
127 5QP 0.491228 0.885714
128 T6P 0.490909 0.767442
129 RZM 0.490909 0.688889
130 NAG MAN BMA 0.485294 0.733333
131 BGC OXZ 0.482759 0.666667
132 IFM BMA 0.482759 0.711111
133 BMA IFM 0.482759 0.711111
134 IFM BGC 0.482759 0.711111
135 9MR 0.482759 0.744186
136 MAL EDO 0.482759 0.942857
137 GLA MAN ABE 0.477612 0.916667
138 A2G GAL 0.47619 0.653061
139 G2F BGC BGC BGC BGC BGC 0.47619 0.868421
140 MAN MMA MAN 0.47619 0.942857
141 GAL NDG 0.47541 0.733333
142 NLC 0.47541 0.733333
143 MAN MNM 0.474576 0.702128
144 FMO 0.474576 0.868421
145 GLC DMJ 0.474576 0.695652
146 NOJ GLC 0.474576 0.695652
147 MAN MAN MAN BMA MAN 0.471429 1
148 XYT 0.467742 0.767442
149 FRU GAL 0.465517 0.842105
150 BMA FRU 0.465517 0.842105
151 W9T 0.465517 0.842105
152 BMA BMA GLA BMA BMA 0.462687 1
153 BMA BMA BMA GLA BMA 0.462687 1
154 MAN MAN MAN MAN MAN MAN MAN MAN 0.4625 0.846154
155 GLC GLC XYP 0.461538 1
156 MAN G63 0.459016 0.653061
157 GDQ GLC 0.459016 0.666667
158 MAN 7D1 0.45614 0.888889
159 GXL 0.454545 0.848485
160 WOO 0.454545 0.848485
161 ALL 0.454545 0.848485
162 MAN 0.454545 0.848485
163 GLC 0.454545 0.848485
164 GAL 0.454545 0.848485
165 GIV 0.454545 0.848485
166 BGC 0.454545 0.848485
167 BMA 0.454545 0.848485
168 GLA 0.454545 0.848485
169 NAG BMA 0.453125 0.653061
170 BGC GAL NAG GAL 0.452055 0.733333
171 GAL NAG GAL GLC 0.452055 0.733333
172 GLA GAL BGC 5VQ 0.451613 0.891892
173 GAL MGC 0.451613 0.702128
174 GLC GLC GLC BGC 0.447761 1
175 GAL NGA GLA BGC GAL 0.447368 0.733333
176 3MG 0.446809 0.857143
177 LAK 0.446429 1
178 MLB 0.446429 1
179 MAN MAN 0.446429 1
180 GLA BMA 0.446429 1
181 KHO 0.446429 0.888889
182 GAL GAL 0.446429 1
183 MAN BMA 0.446429 1
184 GLA BGC 0.446429 1
185 GLA GLC 0.446429 1
186 BGC GLA 0.446429 1
187 BMA GLA 0.446429 1
188 GAL GLC 0.446429 1
189 FUC GAL NAG GAL FUC 0.443038 0.702128
190 MVP 0.442623 0.733333
191 ABL 0.442623 0.702128
192 MAN DGO 0.440678 0.914286
193 LAT NAG GAL 0.44 0.733333
194 GLC GAL NAG GAL 0.44 0.733333
195 OXZ BGC BGC 0.439394 0.6875
196 G2I 0.439394 0.767442
197 G3I 0.439394 0.767442
198 GYP 0.4375 0.857143
199 MMA 0.4375 0.857143
200 AMG 0.4375 0.857143
201 MBG 0.4375 0.857143
202 GAL BGC BGC XYS 0.43662 0.942857
203 ISX 0.433333 0.761905
204 SOR GLC GLC 0.432836 0.970588
205 GLC GLC GLC GLC BGC 0.431034 1
206 GLC GLC GLC GLC GLC BGC 0.431034 1
207 BMA MAN MAN 0.431034 1
208 GLA GAL GLC NBU 0.430769 0.846154
209 BGC GLA GAL FUC 0.430556 0.970588
210 WZ3 0.428571 0.916667
211 8VZ 0.428571 0.673469
212 GAL AAL GAL AAL GAL AAL 0.426667 0.891892
213 GAL NAG GAL NAG GAL NAG 0.426667 0.673469
214 AAL GAL AAL GLA 0.426667 0.891892
215 AAL GAL AAL GAL 0.426667 0.891892
216 NAG GAL GAL NAG 0.426667 0.6875
217 GLC GLC XYS 0.426471 0.970588
218 MAN IFM 0.42623 0.727273
219 GLC IFM 0.42623 0.727273
220 BGC BGC BGC FRU 0.424242 0.868421
221 OPM MAN MAN 0.422535 0.804878
222 XYS BGC BGC BGC BGC XYS BGC BGC BGC 0.421053 0.942857
223 XYS BGC BGC XYS BGC XYS BGC BGC BGC 0.421053 0.942857
224 BGC BGC BGC XYS GAL 0.421053 0.942857
225 BGC BGC BGC XYS BGC BGC 0.421053 0.942857
226 GLO GLC GLC GLC 0.42029 0.970588
227 LSE 0.42029 0.6875
228 SOR GLC GLC GLC 0.42029 0.970588
229 GLC 7LQ 0.419355 0.885714
230 GAL NGT 0.41791 0.66
231 DMU 0.41791 0.785714
232 LMT 0.41791 0.785714
233 UMQ 0.41791 0.785714
234 NGT GAL 0.41791 0.66
235 LMU 0.41791 0.785714
236 TUR 0.416667 0.842105
237 BTU 0.416667 0.842105
238 GLO GLC GLC 0.416667 0.942857
239 GLC FRU 0.416667 0.842105
240 NGA GLA GAL BGC 0.415584 0.733333
241 GLA MMA ABE 0.414286 0.868421
242 FUC BGC GAL NAG GAL 0.411765 0.717391
243 2M8 0.410714 0.911765
244 BGC RAM BGC GAD 0.409639 0.846154
245 GLC BDF 0.40625 0.916667
246 SIA NAG GAL GAL 0.40625 0.622642
247 NAG GAL BGC 0.405405 0.733333
248 GLA MAN RAM ABE 0.405063 0.891892
249 GAL NAG GAL BGC 0.405063 0.702128
250 RIB 0.404762 0.742857
251 FUB 0.404762 0.742857
252 32O 0.404762 0.742857
253 BDR 0.404762 0.742857
254 AHR 0.404762 0.742857
255 Z6J 0.404762 0.742857
256 NAG MAN BMA MAN NAG GAL 0.404494 0.6875
257 M1P 0.403846 0.697674
258 XGP 0.403846 0.697674
259 GL1 0.403846 0.697674
260 G1P 0.403846 0.697674
261 FUC NDG GAL 0.402778 0.717391
262 GAL NAG MAN 0.402778 0.733333
263 GAL NDG FUC 0.402778 0.717391
264 FUC NAG GAL 0.402778 0.717391
265 NAG NAG BMA MAN 0.402439 0.634615
266 FUC GAL 0.4 0.941176
267 LAG 0.4 0.6
268 GAL NAG GAL 0.4 0.702128
269 6UZ 0.4 0.846154
270 RGG 0.4 0.882353
271 GAL BGC NAG GAL 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DKY; Ligand: NOJ; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 5dky.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4AMW 5DI 24.0799
2 3LPP KTL 33.7416
3 3LPP KTL 33.7416
4 3L4U DSK 36.8
5 5NN6 MIG 38.1881
6 3WEO ACR GLC GLC GLC GLC 39.8686
7 3MKK GLC BGC 41.1411
8 3MKK GLC BGC 41.1411
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