Receptor
PDB id Resolution Class Description Source Keywords
5nn6 2 Å EC: 3.2.1.20 CRYSTAL STRUCTURE OF HUMAN LYSOSOMAL ACID-ALPHA-GLUCOSIDASE, COMPLEX WITH N-HYDROXYETHYL-1-DEOXYNOJIRIMYCIN HOMO SAPIENS GLYCOSIDE HYDROLASE LYSOSOME GLYCOGEN CATABOLISM POMPE DIHYDROLASE
Ref.: STRUCTURE OF HUMAN LYSOSOMAL ACID ALPHA-GLUCOSIDASE FOR THE TREATMENT OF POMPE DISEASE. NAT COMMUN V. 8 1111 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1018;
A:1014;
A:1015;
A:1017;
A:1016;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
EDO A:1032;
A:1030;
A:1023;
A:1031;
A:1028;
A:1027;
A:1026;
A:1029;
A:1034;
A:1024;
A:1022;
A:1025;
A:1033;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
NAG NAG D:1;
C:1;
 Invalid;
Invalid;
 none;
none;
 submit data
408.404 n/a O=C(N...
MIG A:1013;
 Valid;
 none;
 Ki = 3 uM
207.224 C8 H17 N O5 C1[C@...
CL A:1020;
A:1019;
A:1021;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
35.453 Cl [Cl-]
PGE A:1038;
A:1037;
A:1035;
A:1036;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
150.173 C6 H14 O4 C(COC...
GOL A:1039;
A:1041;
A:1040;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
NAG NAG BMA E:1;
 Invalid;
 none;
 submit data
570.545 n/a O=C(N...
NAG FUC F:1;
 Invalid;
 none;
 submit data
367.351 n/a O=C(N...
NAG NAG FUC B:1;
 Invalid;
 none;
 submit data
n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NN6 2 Å EC: 3.2.1.20 CRYSTAL STRUCTURE OF HUMAN LYSOSOMAL ACID-ALPHA-GLUCOSIDASE, COMPLEX WITH N-HYDROXYETHYL-1-DEOXYNOJIRIMYCIN HOMO SAPIENS GLYCOSIDE HYDROLASE LYSOSOME GLYCOGEN CATABOLISM POMPE DIHYDROLASE
Ref.: STRUCTURE OF HUMAN LYSOSOMAL ACID ALPHA-GLUCOSIDASE FOR THE TREATMENT OF POMPE DISEASE. NAT COMMUN V. 8 1111 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
2 5NN8 - GLC GLC AC1 n/a n/a
3 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
4 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
2 5NN8 - GLC GLC AC1 n/a n/a
3 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
4 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3W37 - GLC GLC AC1 n/a n/a
2 3WEO Ki = 0.888 uM GLC GLC GLC GLC GLC GLC AC1 n/a n/a
3 3WEL Ki = 2.66 uM GLC GLC GLC AC1 n/a n/a
4 3L4W Ki = 1 uM MIG C8 H17 N O5 C1[C@@H]([....
5 3L4X Ki = 0.13 uM NR3 C12 H24 O12 S2 C1[C@H]([C....
6 3L4Y Ki = 0.1 uM NR4 C12 H24 O12 S2 C1[C@H]([C....
7 3CTT Ki = 0.45 uM 3CU C8 H15 N O5 C1[C@@H]([....
8 3L4V Ki = 0.19 uM KTL C12 H24 O12 S2 C1[C@H]([C....
9 2QMJ Ki = 62 uM GLC GLC AC1 n/a n/a
10 3L4T Ki = 3.8 uM BJ1 C10 H20 O10 S2 C1[C@H]([C....
11 3L4U Ki = 0.03 uM DSK C12 H25 O9 S C1[C@H]([C....
12 3L4Z Ki = 0.19 uM SSD C9 H18 O9 S2 C1[C@H]([C....
13 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
14 5NN8 - GLC GLC AC1 n/a n/a
15 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
16 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
17 3LPP Ki = 0.6 uM KTL C12 H24 O12 S2 C1[C@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MIG; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 MIG 1 1
2 NBV 0.625 0.897959
3 NND 0.543478 0.862745
4 6A9 0.520833 0.846154
Similar Ligands (3D)
Ligand no: 1; Ligand: MIG; Similar ligands found: 413
No: Ligand Similarity coefficient
1 BGC 0.9522
2 8S0 0.9518
3 GLC 0.9447
4 8XQ 0.9409
5 EMZ 0.9386
6 NTZ 0.9360
7 LGC 0.9353
8 CKX 0.9347
9 UEG 0.9342
10 PXL 0.9342
11 GT0 0.9338
12 57O 0.9333
13 3RI 0.9333
14 AMG 0.9331
15 PXM 0.9330
16 NBG 0.9326
17 UAN 0.9318
18 GIM 0.9314
19 AEZ 0.9310
20 HTP 0.9303
21 UQ 0.9301
22 GLA 0.9291
23 GOX 0.9285
24 PFB 0.9282
25 MVL 0.9282
26 GAL 0.9281
27 ALL 0.9273
28 7VJ 0.9264
29 BK9 0.9260
30 MMA 0.9260
31 NDM 0.9249
32 GYP 0.9249
33 CLZ 0.9248
34 5WU 0.9244
35 8GK 0.9244
36 SHG 0.9240
37 G3F 0.9240
38 GCB 0.9239
39 K3Q 0.9227
40 MAN 0.9225
41 2H5 0.9224
42 BMA 0.9223
43 KIB 0.9214
44 7ZE 0.9209
45 MA3 0.9204
46 SYA 0.9197
47 G1P 0.9193
48 BNT 0.9193
49 TEP 0.9191
50 7VS 0.9189
51 FH2 0.9186
52 C2U 0.9182
53 X6X 0.9182
54 GTZ 0.9177
55 4KL 0.9177
56 HPT 0.9176
57 GCS 0.9175
58 UFO 0.9174
59 GAF 0.9173
60 FOT 0.9168
61 GCW 0.9164
62 06B 0.9162
63 SRO 0.9161
64 5WY 0.9160
65 GCU 0.9158
66 M5N 0.9157
67 KG1 0.9150
68 BDP 0.9143
69 EVA 0.9142
70 JXZ 0.9139
71 IJZ 0.9136
72 FSW 0.9130
73 MBG 0.9130
74 2CL 0.9123
75 1GN 0.9118
76 9GP 0.9115
77 9KH 0.9112
78 GLT 0.9111
79 LKA 0.9107
80 CIP 0.9105
81 HLZ 0.9105
82 HHT 0.9103
83 CR1 0.9100
84 0P6 0.9099
85 HNQ 0.9098
86 6LW 0.9098
87 ZWZ 0.9096
88 Q24 0.9096
89 IPT 0.9096
90 FDK 0.9095
91 15L 0.9093
92 IBM 0.9090
93 2FG 0.9088
94 5WX 0.9088
95 FXH 0.9085
96 TFU 0.9084
97 KBG 0.9083
98 E7R 0.9083
99 KJY 0.9079
100 JXW 0.9070
101 9PY 0.9069
102 NPL 0.9067
103 0W8 0.9063
104 149 0.9056
105 AIN 0.9054
106 NOJ 0.9052
107 GIV 0.9052
108 15A 0.9044
109 DBJ 0.9042
110 EJZ 0.9042
111 YO5 0.9041
112 3IT 0.9037
113 ADA 0.9036
114 42C 0.9034
115 CBF 0.9027
116 O2A 0.9027
117 Q6T 0.9026
118 WOO 0.9026
119 MFU 0.9026
120 0LH 0.9022
121 94E 0.9021
122 4ME 0.9021
123 T6Z 0.9016
124 3MG 0.9014
125 3DO 0.9013
126 JTH 0.9012
127 9MG 0.9012
128 PQ0 0.9011
129 PH2 0.9011
130 GFP 0.9011
131 M3S 0.9010
132 OA3 0.9007
133 SOR 0.9006
134 2GS 0.9006
135 HHR 0.9002
136 QAT 0.9001
137 PRZ 0.8998
138 NLA 0.8996
139 Q7A 0.8996
140 M0Q 0.8994
141 7D2 0.8992
142 PRF 0.8990
143 CFF 0.8987
144 OMD 0.8987
145 YIO 0.8985
146 HA7 0.8985
147 091 0.8984
148 HMQ 0.8982
149 GP1 0.8979
150 AKH 0.8978
151 L7T 0.8973
152 TSS 0.8968
153 ZB1 0.8968
154 KP6 0.8966
155 QM1 0.8965
156 3C7 0.8959
157 7MX 0.8958
158 GSY 0.8951
159 GTR 0.8950
160 4HC 0.8947
161 GZ8 0.8947
162 LOG 0.8943
163 9BZ 0.8943
164 6HP 0.8942
165 S3B 0.8942
166 94B 0.8940
167 25W 0.8938
168 JYB 0.8937
169 SR4 0.8932
170 28S 0.8930
171 SFU 0.8929
172 PA1 0.8929
173 GM7 0.8929
174 GDE 0.8925
175 209 0.8918
176 5OF 0.8918
177 MS9 0.8916
178 INS 0.8913
179 KIA 0.8909
180 HKD 0.8909
181 0FK 0.8905
182 LYL 0.8905
183 ASC 0.8902
184 3R6 0.8901
185 GPM 0.8897
186 8WT 0.8897
187 CTS 0.8895
188 MT5 0.8893
189 LIP 0.8892
190 61M 0.8880
191 EGR 0.8880
192 GOG 0.8878
193 DQN 0.8874
194 CKU 0.8872
195 DPZ 0.8871
196 8W9 0.8871
197 6VD 0.8868
198 F52 0.8868
199 C2Y 0.8866
200 Q77 0.8866
201 MQB 0.8864
202 IFL 0.8861
203 KGK 0.8861
204 DEE 0.8861
205 9FQ 0.8861
206 IPD 0.8860
207 RAM 0.8858
208 G6D 0.8858
209 B60 0.8857
210 X05 0.8855
211 B62 0.8855
212 2EC 0.8853
213 23J 0.8853
214 SBK 0.8851
215 4AA 0.8849
216 H33 0.8849
217 H7Y 0.8846
218 1U6 0.8846
219 E7Z 0.8846
220 RNS 0.8844
221 D07 0.8843
222 IAC 0.8838
223 ZZ8 0.8837
224 4VS 0.8837
225 NAG 0.8835
226 AH8 0.8830
227 JYT 0.8830
228 S2T 0.8828
229 92P 0.8828
230 3C1 0.8828
231 6ME 0.8827
232 M3Q 0.8825
233 EXO 0.8825
234 4XV 0.8824
235 EOL 0.8823
236 GXY 0.8821
237 M1H 0.8820
238 4Z4 0.8819
239 L46 0.8818
240 GJS 0.8816
241 LDP 0.8815
242 DJN 0.8815
243 TSR 0.8814
244 5NE 0.8811
245 ISE 0.8809
246 F34 0.8808
247 NPA 0.8805
248 9R5 0.8805
249 C9E 0.8804
250 3C2 0.8803
251 M1Q 0.8803
252 FA3 0.8801
253 790 0.8798
254 MAQ 0.8798
255 2LY 0.8798
256 JND 0.8795
257 512 0.8795
258 DFB 0.8794
259 PMP 0.8794
260 DHY 0.8788
261 329 0.8788
262 ISD 0.8786
263 MAG 0.8784
264 JXN 0.8783
265 N8Y 0.8782
266 ONZ 0.8779
267 ICO 0.8779
268 2FY 0.8777
269 S7B 0.8772
270 DHQ 0.8766
271 GYE 0.8762
272 1QP 0.8758
273 4XS 0.8755
274 NVU 0.8755
275 HQ9 0.8754
276 EV0 0.8754
277 G6P 0.8754
278 VOH 0.8753
279 MUA 0.8751
280 2K8 0.8748
281 L21 0.8748
282 226 0.8747
283 505 0.8745
284 ODO 0.8745
285 JZ4 0.8744
286 8ZE 0.8740
287 1LN 0.8738
288 KDO 0.8738
289 261 0.8737
290 PLP 0.8737
291 D3M 0.8737
292 BEU 0.8736
293 GRX 0.8735
294 82I 0.8734
295 GTL 0.8731
296 DGJ 0.8730
297 HMH 0.8730
298 QMS 0.8729
299 XXR 0.8728
300 HJP 0.8722
301 HHA 0.8722
302 44V 0.8721
303 IOS 0.8721
304 4MX 0.8719
305 20J 0.8716
306 TTY 0.8716
307 2LP 0.8714
308 7ZC 0.8712
309 42J 0.8710
310 ZZZ 0.8708
311 GDL 0.8706
312 1SS 0.8702
313 T9G 0.8702
314 2SX 0.8701
315 6CS 0.8701
316 UNC 0.8699
317 MNP 0.8690
318 SNG 0.8690
319 F69 0.8690
320 AC2 0.8688
321 1N4 0.8688
322 NFM 0.8687
323 2KA 0.8686
324 AX3 0.8686
325 NSG 0.8685
326 RH1 0.8685
327 AMR 0.8684
328 LNR 0.8683
329 FHN 0.8683
330 327 0.8682
331 BM3 0.8679
332 24B 0.8679
333 LTM 0.8679
334 TOF 0.8678
335 K68 0.8675
336 LFR 0.8672
337 PRY 0.8670
338 8VE 0.8669
339 XYP 0.8668
340 MR1 0.8664
341 R9Y 0.8661
342 I4D 0.8660
343 9LI 0.8659
344 ZZT 0.8658
345 CWS 0.8658
346 X04 0.8658
347 FCB 0.8657
348 IF7 0.8656
349 OX2 0.8656
350 O2Y 0.8651
351 X0W 0.8649
352 RM4 0.8647
353 3DM 0.8646
354 BSX 0.8645
355 AS3 0.8645
356 JF1 0.8645
357 0FN 0.8644
358 6DP 0.8644
359 4AV 0.8644
360 DRL 0.8641
361 F5B 0.8641
362 692 0.8640
363 Q71 0.8638
364 2AK 0.8638
365 BCU 0.8636
366 G5V 0.8635
367 7A3 0.8632
368 PQZ 0.8628
369 2MN 0.8628
370 2CZ 0.8625
371 A2G 0.8623
372 PXP 0.8622
373 KUF 0.8619
374 RD4 0.8618
375 8VN 0.8614
376 EPR 0.8612
377 PE0 0.8611
378 ZON 0.8607
379 4RW 0.8600
380 S24 0.8597
381 MEW 0.8594
382 AEH 0.8593
383 I1N 0.8590
384 F5C 0.8590
385 VYM 0.8588
386 5CL 0.8588
387 GNL 0.8588
388 JUG 0.8586
389 AQO 0.8580
390 NGA 0.8578
391 LZM 0.8573
392 12M 0.8572
393 J9W 0.8572
394 PSV 0.8572
395 NSP 0.8571
396 APZ 0.8568
397 AZ8 0.8565
398 15N 0.8565
399 XDE 0.8564
400 42A 0.8562
401 M5K 0.8562
402 8CM 0.8560
403 EV3 0.8558
404 G1O 0.8554
405 MYI 0.8552
406 CFA 0.8551
407 ZPF 0.8549
408 PQK 0.8548
409 NQH 0.8539
410 AJ2 0.8535
411 XQB 0.8530
412 9X5 0.8510
413 RZH 0.8510
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NN6; Ligand: MIG; Similar sites found with APoc: 6
This union binding pocket(no: 1) in the query (biounit: 5nn6.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3MKK GLC BGC 34.5345
2 3MKK BGC GLC 34.5345
3 5DKY NOJ 38.1881
4 5HJO DGO Z61 40.7235
5 5H9O GLC 40.7235
6 5H9O GLC 40.7235
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