Receptor
PDB id Resolution Class Description Source Keywords
2IMA 1.94 Å EC: 3.4.24.69 CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE A LIGHT CHAIN INHI 2,4-DICHLOROCINNAMIC HYDROXAMATE CLOSTRIDIUM BOTULINUM CLOSTRIDIUM BOTULINUM NEUROTOXIN SEROTYPE A PROTEASE INHIBISUBSTRATE SPECIFICITY SUBSTRATE SWITCHING 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
GB4 A:600;
B:600;
 Valid;
Valid;
 none;
none;
 Ki = 300 nM
232.063 C9 H7 Cl2 N O2 c1cc(...
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: GB4; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GB4 1 1
2 TB8 0.541667 1
3 GB5 0.458333 0.9375
Similar Ligands (3D)
Ligand no: 1; Ligand: GB4; Similar ligands found: 474
No: Ligand Similarity coefficient
1 5OO 0.9721
2 HC4 0.9448
3 CFA 0.9441
4 1FE 0.9422
5 HPP 0.9365
6 2HC 0.9359
7 S0W 0.9339
8 P81 0.9335
9 4Z1 0.9316
10 DHC 0.9315
11 QIV 0.9280
12 ENO 0.9257
13 TYR 0.9252
14 TOH 0.9230
15 3SU 0.9227
16 Y3L 0.9213
17 K82 0.9201
18 A6W 0.9194
19 5VU 0.9188
20 AMR 0.9172
21 92G 0.9172
22 DTY 0.9167
23 C4E 0.9165
24 2GQ 0.9161
25 P7Y 0.9153
26 NFM 0.9151
27 0XR 0.9150
28 PLP 0.9143
29 6SD 0.9142
30 DAH 0.9136
31 GVY 0.9135
32 6J5 0.9133
33 IPO 0.9124
34 F06 0.9120
35 P80 0.9119
36 N9J 0.9117
37 3IP 0.9111
38 1BW 0.9109
39 MP5 0.9107
40 4FE 0.9100
41 XCG 0.9095
42 PMP 0.9095
43 TRP 0.9090
44 IOP 0.9087
45 ERZ 0.9086
46 363 0.9084
47 C9M 0.9082
48 0UL 0.9081
49 TMG 0.9080
50 RSV 0.9079
51 4BX 0.9078
52 EQW 0.9078
53 FF2 0.9075
54 5S9 0.9074
55 AJ1 0.9072
56 0K7 0.9064
57 2PV 0.9063
58 S0D 0.9059
59 1V3 0.9057
60 4BF 0.9055
61 F90 0.9055
62 TCA 0.9055
63 H4B 0.9054
64 FT6 0.9053
65 9BF 0.9051
66 1V4 0.9048
67 4HB 0.9046
68 BVS 0.9046
69 I2E 0.9046
70 PFF 0.9043
71 LR2 0.9040
72 ZSP 0.9037
73 C82 0.9036
74 OLU 0.9035
75 PLR 0.9034
76 6C8 0.9032
77 LO1 0.9029
78 4Z9 0.9029
79 4Z3 0.9022
80 JCZ 0.9019
81 AOY 0.9016
82 B1J 0.9015
83 MMS 0.9012
84 JPQ 0.9012
85 BIO 0.9007
86 7L4 0.9004
87 9JT 0.9004
88 AJG 0.9000
89 LVD 0.8999
90 OHJ 0.8993
91 TYC 0.8991
92 833 0.8990
93 FCW 0.8989
94 5TO 0.8986
95 ZEA 0.8983
96 2FX 0.8983
97 5WN 0.8981
98 6HP 0.8979
99 6Q3 0.8977
100 2PK 0.8973
101 FMQ 0.8973
102 H75 0.8967
103 JA5 0.8966
104 PH3 0.8963
105 PXP 0.8961
106 IYR 0.8956
107 H2B 0.8955
108 4AB 0.8954
109 HCI 0.8954
110 AVX 0.8954
111 PIQ 0.8951
112 3D8 0.8950
113 PO6 0.8950
114 KLS 0.8950
115 CXH 0.8945
116 4I8 0.8944
117 SWX 0.8944
118 KMY 0.8943
119 0DF 0.8939
120 EE8 0.8938
121 A5H 0.8937
122 20D 0.8935
123 NAG 0.8935
124 GJK 0.8932
125 109 0.8932
126 CX4 0.8932
127 P4L 0.8931
128 SX2 0.8931
129 A9B 0.8931
130 4CF 0.8929
131 BG6 0.8929
132 F40 0.8927
133 DFL 0.8927
134 JBZ 0.8926
135 DTR 0.8923
136 HJH 0.8923
137 XIZ 0.8922
138 0OK 0.8922
139 5O6 0.8917
140 4CN 0.8914
141 C53 0.8911
142 9NB 0.8911
143 A7H 0.8907
144 CBE 0.8907
145 6P3 0.8907
146 FER 0.8906
147 M78 0.8904
148 X04 0.8903
149 1HP 0.8903
150 B41 0.8899
151 HBI 0.8898
152 G6P 0.8896
153 1V1 0.8894
154 FTV 0.8894
155 NFA 0.8893
156 OQC 0.8893
157 IQW 0.8891
158 657 0.8890
159 5H6 0.8890
160 TYE 0.8890
161 ZIP 0.8889
162 F5C 0.8889
163 A7K 0.8889
164 3ZB 0.8888
165 GO2 0.8887
166 BQ2 0.8886
167 FZM 0.8886
168 2P3 0.8885
169 PHI 0.8885
170 397 0.8884
171 A51 0.8883
172 7AP 0.8881
173 3VX 0.8880
174 IS2 0.8875
175 6C9 0.8875
176 HL4 0.8875
177 OOG 0.8873
178 L03 0.8872
179 A73 0.8872
180 N7I 0.8871
181 RKV 0.8871
182 E3X 0.8870
183 SZ5 0.8870
184 PBN 0.8868
185 BHS 0.8866
186 LZ5 0.8863
187 3F4 0.8863
188 878 0.8863
189 NIF 0.8861
190 6ZX 0.8861
191 GJB 0.8861
192 UAY 0.8859
193 S8P 0.8858
194 4NR 0.8856
195 A6P 0.8856
196 2K8 0.8855
197 1A7 0.8854
198 80G 0.8852
199 RGK 0.8852
200 S60 0.8852
201 GO8 0.8850
202 0NX 0.8849
203 ZHA 0.8841
204 6KT 0.8841
205 CPZ 0.8840
206 Q0K 0.8840
207 8YH 0.8840
208 BGU 0.8840
209 WLH 0.8839
210 6C5 0.8838
211 2LT 0.8838
212 3H2 0.8836
213 68B 0.8834
214 S7S 0.8834
215 C0W 0.8834
216 4BY 0.8834
217 N91 0.8832
218 F18 0.8832
219 U13 0.8832
220 XI7 0.8831
221 HWD 0.8829
222 TID 0.8829
223 PPY 0.8828
224 5E5 0.8826
225 6N4 0.8825
226 D1Y 0.8823
227 EUH 0.8822
228 M6P 0.8822
229 0SY 0.8822
230 2D2 0.8822
231 7EH 0.8821
232 X48 0.8821
233 25F 0.8819
234 KTW 0.8819
235 YIP 0.8818
236 6MW 0.8818
237 EUE 0.8817
238 QME 0.8817
239 RVE 0.8816
240 BBY 0.8815
241 6DQ 0.8815
242 TU0 0.8814
243 MD6 0.8814
244 ALE 0.8813
245 BGN 0.8812
246 55D 0.8810
247 VM1 0.8810
248 F4K 0.8810
249 5NN 0.8808
250 S98 0.8806
251 HHS 0.8805
252 7PJ 0.8805
253 ZEC 0.8804
254 FHV 0.8802
255 5TZ 0.8801
256 D9Z 0.8800
257 5B2 0.8799
258 2WU 0.8798
259 H35 0.8797
260 5RP 0.8797
261 UNJ 0.8797
262 NFZ 0.8795
263 RDV 0.8795
264 2JX 0.8794
265 KYN 0.8794
266 GZV 0.8793
267 YPN 0.8792
268 4BL 0.8790
269 ARG 0.8790
270 ZYQ 0.8789
271 7FU 0.8788
272 4AF 0.8788
273 4FC 0.8787
274 14W 0.8787
275 A05 0.8787
276 JSX 0.8786
277 6FG 0.8786
278 GLP 0.8786
279 M3W 0.8784
280 1EB 0.8783
281 ZRK 0.8781
282 36Y 0.8779
283 ESI 0.8779
284 HXY 0.8779
285 96Z 0.8776
286 27K 0.8775
287 N4E 0.8774
288 STZ 0.8774
289 STT 0.8773
290 FCD 0.8773
291 3VS 0.8772
292 E9L 0.8771
293 NK5 0.8771
294 50C 0.8771
295 5V7 0.8769
296 NAL 0.8769
297 DVK 0.8769
298 N1E 0.8767
299 PZP 0.8766
300 NPS 0.8766
301 AJD 0.8764
302 BP7 0.8763
303 HH6 0.8762
304 K7H 0.8757
305 SNV 0.8756
306 2QC 0.8756
307 SYE 0.8756
308 A5E 0.8756
309 4LW 0.8756
310 28A 0.8754
311 BDI 0.8754
312 OJM 0.8753
313 3GX 0.8752
314 P4T 0.8751
315 RES 0.8749
316 TZP 0.8748
317 EES 0.8747
318 K80 0.8743
319 AP6 0.8743
320 SJR 0.8741
321 GGB 0.8740
322 D8Q 0.8739
323 DXK 0.8738
324 ESX 0.8738
325 5LA 0.8732
326 0ON 0.8732
327 NKI 0.8732
328 PRL 0.8731
329 3VQ 0.8731
330 CHQ 0.8730
331 KP2 0.8730
332 CDJ 0.8727
333 S0A 0.8726
334 7MW 0.8721
335 G14 0.8720
336 MSR 0.8720
337 II4 0.8718
338 613 0.8718
339 API 0.8717
340 N9M 0.8715
341 C1M 0.8715
342 37E 0.8714
343 YE7 0.8713
344 6C4 0.8712
345 IOS 0.8711
346 5ER 0.8710
347 61M 0.8709
348 P93 0.8708
349 Z70 0.8708
350 5F5 0.8706
351 ODK 0.8705
352 CIY 0.8704
353 8NX 0.8703
354 3IL 0.8702
355 VT3 0.8702
356 YX1 0.8701
357 AVA 0.8701
358 7OD 0.8700
359 LSQ 0.8699
360 LL1 0.8696
361 78Y 0.8695
362 IAC 0.8695
363 PH2 0.8694
364 R5P 0.8693
365 TJM 0.8691
366 RA7 0.8690
367 1XS 0.8690
368 HL6 0.8687
369 B21 0.8685
370 5TT 0.8685
371 7EL 0.8684
372 AOT 0.8684
373 68A 0.8681
374 ZRL 0.8680
375 GJG 0.8679
376 SJK 0.8675
377 S0E 0.8675
378 VC3 0.8674
379 J6W 0.8673
380 1KN 0.8672
381 1PS 0.8672
382 5TY 0.8671
383 6FB 0.8670
384 1SF 0.8669
385 7N8 0.8668
386 GXD 0.8667
387 GXG 0.8666
388 27F 0.8666
389 S7D 0.8664
390 J27 0.8663
391 1Q4 0.8660
392 KWB 0.8658
393 OJD 0.8657
394 EYV 0.8656
395 6H2 0.8656
396 6QT 0.8655
397 ESP 0.8655
398 HX4 0.8654
399 4R1 0.8653
400 XIF XYP 0.8652
401 272 0.8652
402 K3D 0.8651
403 9CE 0.8651
404 LEL 0.8649
405 SB7 0.8649
406 SSY 0.8648
407 R52 0.8648
408 KLE 0.8646
409 ZTW 0.8644
410 ZZA 0.8643
411 0FR 0.8642
412 P7V 0.8641
413 4FP 0.8641
414 4FF 0.8639
415 8D6 0.8636
416 HNT 0.8635
417 J1K 0.8632
418 GT1 0.8630
419 4ZF 0.8628
420 Q5M 0.8627
421 E9S 0.8624
422 HPX 0.8623
423 LI7 0.8622
424 JMG 0.8620
425 5M2 0.8618
426 R2P 0.8618
427 91F 0.8615
428 3R4 0.8615
429 7G0 0.8612
430 5F8 0.8612
431 XYP XIF 0.8612
432 5FL 0.8612
433 EZL 0.8609
434 JAH 0.8608
435 1QV 0.8607
436 HSX 0.8605
437 LJ1 0.8604
438 3NM 0.8602
439 CX6 0.8601
440 3Y7 0.8600
441 08C 0.8599
442 52F 0.8597
443 SNU 0.8597
444 YE6 0.8596
445 3WK 0.8596
446 B61 0.8594
447 M4E 0.8592
448 NY4 0.8591
449 A63 0.8589
450 LJ2 0.8585
451 YZ9 0.8582
452 5P3 0.8580
453 GHQ 0.8580
454 1UZ 0.8578
455 1A5 0.8578
456 WA1 0.8577
457 428 0.8577
458 KWV 0.8573
459 NIY 0.8567
460 LJ3 0.8565
461 V1T 0.8564
462 CG 0.8559
463 CTE 0.8557
464 26C 0.8557
465 M6D 0.8557
466 8V8 0.8555
467 NPX 0.8553
468 D6G 0.8552
469 1ZC 0.8547
470 MFZ 0.8546
471 O2Y 0.8535
472 8NB 0.8535
473 7MX 0.8534
474 THU 0.8532
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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