Receptor
PDB id Resolution Class Description Source Keywords
2ILP 1.9 Å EC: 3.4.24.69 CLOSTRIDIUM BOTULINUM SEROTYPE A LIGHT CHAIN INHIBITED BY 4- CHLOROCINNAMIC HYDROXAMATE CLOSTRIDIUM BOTULINUM CLOSTRIDIUM BOTULINUM NEUROTOXIN TYPE A SUBSTRATE SPECIFICSUBSTRATE SWITCHING PROTEASE INHIBITORS HYDROLASE
Ref.: STRUCTURES OF CLOSTRIDIUM BOTULINUM NEUROTOXIN SERO LIGHT CHAIN COMPLEXED WITH SMALL-MOLECULE INHIBITOR HIGHLIGHT ACTIVE-SITE FLEXIBILITY. CHEM.BIOL. V. 14 533 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GB5 A:600;
B:600;
 Valid;
Valid;
 none;
none;
 ic50 = 15 uM
197.618 C9 H8 Cl N O2 c1cc(...
PO4 A:501;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
ZN A:500;
B:500;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3C88 1.6 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF BOTULINUM NEURO SEROTYPE A WITH INHIBITORY PEPTIDE RRGC CLOSTRIDIUM BOTULINUM BOTULINUM NEUROTOXIN TYPE A CATALYTIC DOMAIN ENDOPEPTIDASEWARFARE AGENT PROTEASE SECRETED HYDROLASE-HYDROLASE INHICOMPLEX
Ref.: STRUCTURE- AND SUBSTRATE-BASED INHIBITOR DESIGN FOR CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE A J.BIOL.CHEM. V. 283 18883 2008
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638.1 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638.1 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3DDB ic50 = 94.9 uM ARG ARG ALA THR LYS MET NH2 n/a n/a
2 2G7Q - AHL C6 H15 N5 O2 [H]/N=C(N)....
3 5V8U - 90M C12 H12 F N3 O S Cc1c(n[nH]....
4 3QJ0 Ki = 6.3 uM QI3 C17 H16 Cl2 N2 O5 S c1cc(ccc1O....
5 3NF3 Ki = 638.1 nM ARG ARG PHE AIB ALA MET LEU ALA n/a n/a
6 3QIZ Ki = 6.1 uM QI2 C24 H32 F2 N2 O3 Cc1cc(ccc1....
7 6XCF - UZP C16 H22 Cl2 N2 O3 CCCCCNC(=O....
8 6XCE - UZM C14 H18 Cl2 N2 O3 S c1cc(c(cc1....
9 2IMB - AHL C6 H15 N5 O2 [H]/N=C(N)....
10 5V8P Ki = 10.2 uM 90G C11 H10 Cl N3 O S c1cc(ccc1c....
11 2ILP ic50 = 15 uM GB5 C9 H8 Cl N O2 c1cc(ccc1C....
12 3DS9 - 01W ARG TRP THR DAB MET LEU GLY n/a n/a
13 5V8R - 90J C11 H10 F N3 O S c1cc(ccc1c....
14 3C8B Ki = 786 nM ARG ARG GLY ILE NH2 n/a n/a
15 3C89 Ki = 845 nM ARG ARG GLY MET NH2 n/a n/a
16 3C8A Ki = 660 nM ARG ARG GLY LEU NH2 n/a n/a
17 3QIY Ki = 4.6 uM QI1 C18 H20 Cl2 N2 O2 c1cc(ccc1C....
18 3C88 Ki = 157 nM ARG ARG GLY CYS NH2 n/a n/a
19 2IMA Ki = 300 nM GB4 C9 H7 Cl2 N O2 c1cc(c(cc1....
20 3BOO Ki = 1.9 uM ACE CSO ARG ALA THR LYS MET LEU n/a n/a
21 4HEV Ki = 460 nM AXM C12 H19 N O2 C1C2CC3CC1....
22 3DDA ic50 = 132.9 uM GLN ARG ALA THR LYS MET NH2 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GB5; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 GB5 1 1
2 C65 0.48 0.684211
3 GB4 0.458333 0.9375
4 TB8 0.416667 0.9375
5 FG8 0.413793 0.789474
Similar Ligands (3D)
Ligand no: 1; Ligand: GB5; Similar ligands found: 426
No: Ligand Similarity coefficient
1 HC4 0.9704
2 HPP 0.9597
3 P81 0.9541
4 S0W 0.9496
5 GVY 0.9434
6 0XR 0.9430
7 N9J 0.9420
8 JA5 0.9410
9 DHC 0.9398
10 5OO 0.9384
11 1FE 0.9379
12 92G 0.9374
13 B1J 0.9368
14 TCA 0.9365
15 KLS 0.9365
16 S0D 0.9364
17 QIV 0.9352
18 ENO 0.9350
19 TYR 0.9336
20 OLU 0.9332
21 XCG 0.9295
22 TOH 0.9277
23 4BX 0.9274
24 XIZ 0.9268
25 6SD 0.9265
26 0K7 0.9259
27 DTY 0.9256
28 E3X 0.9254
29 I2E 0.9252
30 Y3L 0.9242
31 4FE 0.9237
32 L03 0.9231
33 ARG 0.9212
34 2FX 0.9207
35 PBN 0.9207
36 CFA 0.9201
37 2PV 0.9200
38 TYC 0.9196
39 LO1 0.9196
40 SX2 0.9195
41 IPO 0.9193
42 P80 0.9188
43 TMG 0.9187
44 ERZ 0.9184
45 4HB 0.9178
46 TID 0.9173
47 4Z1 0.9166
48 LVD 0.9165
49 F90 0.9159
50 BVS 0.9155
51 FF2 0.9150
52 HCI 0.9149
53 3H2 0.9147
54 SWX 0.9143
55 C82 0.9142
56 JCZ 0.9142
57 OJM 0.9136
58 FZM 0.9131
59 OOG 0.9129
60 PO6 0.9125
61 TYE 0.9121
62 5VU 0.9117
63 0UL 0.9117
64 5TO 0.9116
65 0NX 0.9115
66 2PK 0.9110
67 HL6 0.9105
68 PPY 0.9103
69 68B 0.9100
70 API 0.9093
71 6CL 0.9090
72 80G 0.9090
73 8YH 0.9088
74 KLE 0.9083
75 NFZ 0.9082
76 6N4 0.9080
77 S7S 0.9079
78 36M 0.9079
79 4YZ 0.9077
80 U13 0.9076
81 EQW 0.9075
82 AOY 0.9073
83 STV 0.9072
84 6C8 0.9070
85 PFF 0.9070
86 YIP 0.9070
87 CXH 0.9070
88 4LW 0.9069
89 M1T 0.9067
90 DVK 0.9066
91 0ON 0.9065
92 PLP 0.9060
93 RA7 0.9059
94 27K 0.9059
95 1EB 0.9059
96 GVA 0.9058
97 7FU 0.9053
98 C4E 0.9053
99 RSV 0.9053
100 A6W 0.9051
101 F18 0.9049
102 XOG 0.9049
103 3IP 0.9049
104 CIR 0.9049
105 A51 0.9047
106 795 0.9047
107 5H6 0.9040
108 PH3 0.9036
109 1PS 0.9030
110 397 0.9028
111 FHV 0.9028
112 GGB 0.9027
113 S0A 0.9026
114 5LA 0.9026
115 P7Y 0.9024
116 ENW 0.9022
117 QME 0.9020
118 4BF 0.9018
119 DAH 0.9018
120 FER 0.9018
121 CPZ 0.9017
122 833 0.9017
123 6P3 0.9013
124 6J5 0.9012
125 36Y 0.9007
126 3VQ 0.9000
127 WA1 0.8999
128 A5E 0.8998
129 363 0.8997
130 ZEC 0.8993
131 GJK 0.8987
132 37E 0.8987
133 AJG 0.8986
134 JBZ 0.8986
135 LZ5 0.8986
136 5S9 0.8984
137 IS2 0.8979
138 PHI 0.8977
139 KMY 0.8977
140 NOT 0.8974
141 PML 0.8974
142 2QC 0.8973
143 XI7 0.8972
144 6ZX 0.8971
145 Z70 0.8971
146 N9M 0.8971
147 JAH 0.8969
148 1BW 0.8969
149 DAR 0.8968
150 IYR 0.8968
151 6C5 0.8966
152 ZRK 0.8966
153 HX4 0.8963
154 X48 0.8960
155 ZTW 0.8958
156 GO2 0.8957
157 2HC 0.8948
158 PBA 0.8948
159 6MW 0.8948
160 7MW 0.8946
161 C53 0.8945
162 9JT 0.8940
163 4CF 0.8938
164 3VS 0.8934
165 0SY 0.8933
166 AJ1 0.8932
167 HFA 0.8932
168 2P3 0.8931
169 ZEA 0.8929
170 PHE 0.8929
171 ODK 0.8928
172 5RP 0.8927
173 AOT 0.8924
174 PQM 0.8923
175 3ZB 0.8921
176 JMG 0.8920
177 1XS 0.8920
178 RP3 0.8920
179 HJD 0.8917
180 C9M 0.8917
181 SB7 0.8915
182 4FC 0.8913
183 K7H 0.8913
184 G14 0.8911
185 R5P 0.8910
186 LR2 0.8910
187 OHJ 0.8909
188 VC3 0.8909
189 5O6 0.8908
190 EQA 0.8906
191 F4K 0.8906
192 N1E 0.8904
193 BP7 0.8900
194 61M 0.8899
195 K3D 0.8899
196 7OD 0.8896
197 6H2 0.8896
198 BQ2 0.8895
199 OJD 0.8894
200 613 0.8892
201 A7H 0.8890
202 PQS 0.8889
203 NY4 0.8888
204 D8Q 0.8886
205 AVX 0.8885
206 F4E 0.8882
207 GOE 0.8882
208 9NB 0.8882
209 SOJ 0.8880
210 A5H 0.8879
211 UNJ 0.8876
212 28A 0.8875
213 50C 0.8875
214 3SU 0.8874
215 E4P 0.8870
216 FMQ 0.8870
217 NFA 0.8868
218 LPA 0.8865
219 3VX 0.8864
220 TRP 0.8863
221 L2K 0.8860
222 2JX 0.8859
223 4LV 0.8859
224 MSR 0.8859
225 YPN 0.8857
226 RES 0.8854
227 4CN 0.8853
228 6C4 0.8852
229 A9B 0.8850
230 4I8 0.8849
231 LSQ 0.8847
232 SJR 0.8847
233 HL4 0.8847
234 IOP 0.8847
235 6C9 0.8846
236 ZE7 0.8843
237 9BF 0.8843
238 4UM 0.8843
239 N91 0.8842
240 MJW 0.8842
241 26P 0.8841
242 ESX 0.8839
243 PIQ 0.8838
244 J1K 0.8838
245 7EH 0.8836
246 PRL 0.8833
247 4BY 0.8825
248 7KE 0.8823
249 5OR 0.8821
250 8CC 0.8816
251 AHN 0.8815
252 650 0.8815
253 6KT 0.8815
254 DPN 0.8812
255 0DF 0.8811
256 GJG 0.8810
257 2LT 0.8808
258 SNU 0.8808
259 M78 0.8807
260 6L6 0.8803
261 1Q2 0.8803
262 NK5 0.8803
263 I3E 0.8802
264 ALE 0.8798
265 5E5 0.8795
266 ZHA 0.8793
267 H4B 0.8793
268 ZZA 0.8793
269 4FP 0.8792
270 ICB 0.8788
271 3R4 0.8787
272 RKV 0.8783
273 ESP 0.8782
274 IJ6 0.8779
275 64Z 0.8779
276 LYS 0.8778
277 6FG 0.8776
278 47V 0.8776
279 LR8 0.8775
280 6FB 0.8774
281 4AF 0.8773
282 4Z3 0.8772
283 LJ2 0.8771
284 HRG 0.8769
285 X0U 0.8768
286 5TT 0.8768
287 K82 0.8766
288 1HP 0.8765
289 MMS 0.8764
290 URO 0.8762
291 J6W 0.8762
292 L22 0.8761
293 ZSP 0.8759
294 EUH 0.8758
295 P4T 0.8756
296 4Z9 0.8755
297 HH6 0.8754
298 EES 0.8746
299 R9J 0.8744
300 CIY 0.8741
301 109 0.8740
302 6Q3 0.8739
303 KNA 0.8738
304 UAY 0.8737
305 4XF 0.8734
306 EP1 0.8733
307 2D2 0.8732
308 DEZ 0.8731
309 PLR 0.8728
310 MD6 0.8726
311 4FF 0.8725
312 QBP 0.8722
313 HBI 0.8721
314 RCV 0.8721
315 HPX 0.8720
316 SSB 0.8720
317 ESJ 0.8719
318 7VP 0.8719
319 FCW 0.8717
320 1L5 0.8714
321 TZP 0.8714
322 MF3 0.8713
323 5B2 0.8712
324 P7V 0.8711
325 N7I 0.8710
326 BZ2 0.8709
327 011 0.8708
328 BIO 0.8706
329 7N8 0.8706
330 H2B 0.8704
331 MKN 0.8703
332 OCA 0.8700
333 YZM 0.8697
334 4BL 0.8697
335 492 0.8695
336 LJ1 0.8693
337 56D 0.8690
338 JSX 0.8690
339 GHQ 0.8689
340 4AB 0.8687
341 F02 0.8685
342 ZYC 0.8683
343 7G0 0.8682
344 0L1 0.8682
345 C1M 0.8682
346 SPD 0.8681
347 F06 0.8681
348 4AU 0.8678
349 2WU 0.8677
350 HNT 0.8674
351 R2P 0.8673
352 EZL 0.8673
353 AES 0.8672
354 EYV 0.8672
355 BHS 0.8669
356 245 0.8667
357 BSU 0.8663
358 8V8 0.8662
359 ZRL 0.8660
360 JPQ 0.8657
361 RGP 0.8654
362 4V2 0.8653
363 OQC 0.8651
364 3D3 0.8649
365 G6P 0.8648
366 LJ3 0.8647
367 PRA 0.8645
368 7PJ 0.8645
369 4NP 0.8643
370 CBE 0.8642
371 A5P 0.8641
372 5ER 0.8639
373 90G 0.8638
374 JGB 0.8636
375 428 0.8632
376 P93 0.8630
377 ZIP 0.8629
378 MR4 0.8625
379 1A7 0.8625
380 STL 0.8623
381 MR5 0.8623
382 D3G 0.8614
383 1X4 0.8611
384 AMR 0.8611
385 AKG 0.8609
386 PNP 0.8606
387 ITE 0.8602
388 8D6 0.8601
389 A6P 0.8600
390 RYV 0.8599
391 GO8 0.8597
392 DFL 0.8593
393 78Y 0.8591
394 HSX 0.8587
395 0FR 0.8586
396 BG6 0.8584
397 CHQ 0.8584
398 SZ5 0.8583
399 268 0.8583
400 RGK 0.8582
401 L1T 0.8582
402 FMH 0.8579
403 20D 0.8578
404 5TY 0.8577
405 3F4 0.8573
406 2K8 0.8571
407 WV7 0.8565
408 NKI 0.8565
409 S7D 0.8564
410 NE2 0.8559
411 4NS 0.8554
412 5M2 0.8553
413 1V1 0.8551
414 Q0K 0.8550
415 3D8 0.8545
416 25F 0.8539
417 HRM 0.8534
418 38E 0.8531
419 3N0 0.8530
420 BVB 0.8530
421 X6W 0.8526
422 BX4 0.8526
423 MPV 0.8525
424 A73 0.8525
425 D9Z 0.8518
426 ONH 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3C88; Ligand: ARG ARG GLY CYS NH2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3c88.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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