Receptor
PDB id Resolution Class Description Source Keywords
3R4S 2.15 Å EC: 3.4.24.69 CELL ENTRY OF BOTULINUM NEUROTOXIN TYPE C IS DEPENDENT UPON INTERACTION WITH TWO GANGLIOSIDE MOLECULES CLOSTRIDIUM BOTULINUM BOTULINUM TOXINS GANGLIOSIDES HYDROLASE
Ref.: THE BIOLOGICAL ACTIVITY OF BOTULINUM NEUROTOXIN TYP DEPENDENT UPON NOVEL TYPES OF GANGLIOSIDE BINDING S MOL.MICROBIOL. V. 81 143 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SIA A:6859;
B:6859;
Valid;
Valid;
none;
none;
submit data
309.27 C11 H19 N O9 CC(=O...
SLB A:6875;
B:6875;
Valid;
Valid;
none;
none;
submit data
309.27 C11 H19 N O9 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3R4S 2.15 Å EC: 3.4.24.69 CELL ENTRY OF BOTULINUM NEUROTOXIN TYPE C IS DEPENDENT UPON INTERACTION WITH TWO GANGLIOSIDE MOLECULES CLOSTRIDIUM BOTULINUM BOTULINUM TOXINS GANGLIOSIDES HYDROLASE
Ref.: THE BIOLOGICAL ACTIVITY OF BOTULINUM NEUROTOXIN TYP DEPENDENT UPON NOVEL TYPES OF GANGLIOSIDE BINDING S MOL.MICROBIOL. V. 81 143 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3R4S - SLB C11 H19 N O9 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3R4S - SLB C11 H19 N O9 CC(=O)N[C@....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5TPC Kd = 0.3 mM GAL SIA NGA GAL SIA n/a n/a
2 3R4S - SLB C11 H19 N O9 CC(=O)N[C@....
3 3OBT - SLB C11 H19 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA; Similar ligands found: 49
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 18D 0.758621 0.955556
4 42D 0.758621 0.875
5 NGC 0.754386 0.933333
6 MNA 0.629032 0.895833
7 79J 0.615385 0.934783
8 SIA CMO 0.59375 0.877551
9 CNP 0.58209 0.875
10 KDN 0.568965 0.72093
11 KDM 0.568965 0.72093
12 SIA SIA 0.565789 0.826923
13 SLB SIA 0.565789 0.826923
14 SIA SIA SIA SLB 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 SLB SIA SIA SIA SIA 0.558442 0.826923
17 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
18 FSI 0.515152 0.895833
19 SFJ 0.5 0.875
20 6KL 0.5 0.807692
21 MN0 0.485714 0.895833
22 EQP 0.470588 0.788462
23 AXP 0.470588 0.788462
24 GAL SIA 0.469136 0.843137
25 SIA GAL 0.463415 0.86
26 SID 0.459459 0.82
27 SIA SIA SIA 0.453488 0.826923
28 MUS 0.449438 0.796296
29 NXD 0.447368 0.792453
30 SIA 2FG 0.447059 0.796296
31 SIA WIA 0.447059 0.767857
32 SLT 0.44086 0.877551
33 KDO 0.435484 0.704545
34 SIA NAG 0.430233 0.781818
35 4U0 0.427083 0.86
36 4U2 0.425532 0.843137
37 BND 0.416667 0.807692
38 SKD 0.414286 0.875
39 SIA SIA GAL 0.410526 0.811321
40 4U1 0.408163 0.826923
41 GLA GLC SIA 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 SIA BGC GAL 0.402062 0.86
44 BGC GAL SIA 0.402062 0.86
45 SIA GAL GLC 0.402062 0.86
46 BGC SIA GAL 0.402062 0.86
47 SIA GAL BGC 0.402062 0.86
48 4AM 0.4 0.833333
49 DAN 0.4 0.911111
Ligand no: 2; Ligand: SLB; Similar ligands found: 49
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 18D 0.758621 0.955556
4 42D 0.758621 0.875
5 NGC 0.754386 0.933333
6 MNA 0.629032 0.895833
7 79J 0.615385 0.934783
8 SIA CMO 0.59375 0.877551
9 CNP 0.58209 0.875
10 KDN 0.568965 0.72093
11 KDM 0.568965 0.72093
12 SIA SIA 0.565789 0.826923
13 SLB SIA 0.565789 0.826923
14 SIA SIA SIA SLB 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 SLB SIA SIA SIA SIA 0.558442 0.826923
17 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
18 FSI 0.515152 0.895833
19 SFJ 0.5 0.875
20 6KL 0.5 0.807692
21 MN0 0.485714 0.895833
22 EQP 0.470588 0.788462
23 AXP 0.470588 0.788462
24 GAL SIA 0.469136 0.843137
25 SIA GAL 0.463415 0.86
26 SID 0.459459 0.82
27 SIA SIA SIA 0.453488 0.826923
28 MUS 0.449438 0.796296
29 NXD 0.447368 0.792453
30 SIA 2FG 0.447059 0.796296
31 SIA WIA 0.447059 0.767857
32 SLT 0.44086 0.877551
33 KDO 0.435484 0.704545
34 SIA NAG 0.430233 0.781818
35 4U0 0.427083 0.86
36 4U2 0.425532 0.843137
37 BND 0.416667 0.807692
38 SKD 0.414286 0.875
39 SIA SIA GAL 0.410526 0.811321
40 4U1 0.408163 0.826923
41 GLA GLC SIA 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 SIA BGC GAL 0.402062 0.86
44 BGC GAL SIA 0.402062 0.86
45 SIA GAL GLC 0.402062 0.86
46 BGC SIA GAL 0.402062 0.86
47 SIA GAL BGC 0.402062 0.86
48 4AM 0.4 0.833333
49 DAN 0.4 0.911111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3R4S; Ligand: SIA; Similar sites found: 74
This union binding pocket(no: 1) in the query (biounit: 3r4s.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3C1X CKK 0.026 0.40317 1.34048
2 4L80 1VU 0.03795 0.40389 1.72414
3 5JFL NAD 0.04777 0.40419 2.0316
4 3HGM ATP 0.01422 0.40204 2.04082
5 1ZVW PRP 0.01693 0.40793 2.1164
6 1TIW FAD 0.02638 0.41782 2.25734
7 1TIW TFB 0.02638 0.41782 2.25734
8 4O8A FAD 0.02334 0.41269 2.25734
9 5KF6 FAD 0.03022 0.40824 2.25734
10 5KF6 TFB 0.03022 0.40824 2.25734
11 5TZ9 7SD 0.01426 0.41867 2.28137
12 2FHJ H4Z 0.009398 0.42223 2.36486
13 3HAZ FAD 0.03336 0.4028 2.48307
14 2WZV FMN 0.03339 0.40704 2.55319
15 2QBU SAH 0.003913 0.43332 2.58621
16 5D4V SAH 0.02187 0.40347 2.61194
17 3DCJ THH 0.005339 0.4361 2.7907
18 1GAR U89 0.04001 0.40227 2.83019
19 2E1T MLC 0.02146 0.40888 2.93454
20 5GS9 ARG 0.007412 0.42916 2.96736
21 5VYR B62 0.0006757 0.49621 3.06513
22 5VYR GMP 0.0006757 0.49621 3.06513
23 1GSA ADP 0.01774 0.40514 3.16456
24 2AKO ADP 0.01023 0.41928 3.18725
25 5BV3 M7G 0.01697 0.40164 3.18841
26 4GLW NMN 0.001107 0.44237 3.27869
27 4ANP 3QI 0.002311 0.46797 3.39506
28 3OZ2 OZ2 0.01943 0.41702 3.52645
29 4LXQ FON 0.001068 0.49297 3.64964
30 4LXQ TYD 0.001068 0.49297 3.64964
31 4KWI 1TJ 0.04773 0.40497 3.80228
32 4KWI NAP 0.04626 0.40497 3.80228
33 4FFG LBS 0.00164 0.40711 3.83747
34 2X00 GYN 0.01125 0.41651 3.96476
35 2Q7V FAD 0.01443 0.44974 4
36 3AB4 THR 0.007878 0.41158 4.038
37 3BC9 ACR 0.01822 0.40291 4.06321
38 3HMO STU 0.01594 0.40331 4.09357
39 2DT9 THR 0.00389 0.42057 4.19162
40 4DHY S41 0.0005875 0.5017 4.28894
41 3HY9 098 0.03072 0.40038 4.52489
42 3KRL KRL 0.02289 0.40635 4.77612
43 4UCI ADN 0.0055 0.41035 4.81928
44 4L2I FAD 0.03402 0.40112 4.94297
45 4L2I NAD 0.04568 0.40112 4.94297
46 4JWJ SAH 0.01899 0.40467 4.9505
47 2V95 HCY 0.01041 0.40745 5.12129
48 2FV5 541 0.01693 0.42492 5.36398
49 3ZRM ZRM 0.009636 0.4154 5.39084
50 2VAP GDP 0.01384 0.42967 5.49451
51 3N2S FMN 0.01652 0.40887 5.62249
52 1TLC DGP 0.01194 0.40806 5.66038
53 1GTE FMN 0.03395 0.40937 6.32054
54 1I52 CTP 0.02928 0.41491 6.35593
55 1DQX BMP 0.03599 0.40009 6.36704
56 4ZX2 4TE 0.01155 0.40452 6.60661
57 1RC0 KT5 0.002704 0.45204 6.69856
58 1P9P SAH 0.03081 0.40166 7.27969
59 4B7X NAP 0.02845 0.40032 7.44048
60 3G5S FAD 0.03982 0.4015 7.90068
61 5MVR ADP 0.01019 0.41354 8.02469
62 4MO4 ACP 0.03389 0.40026 8.35579
63 4X7Y SAH 0.03829 0.40259 8.75912
64 5VYQ FON 0.00005994 0.41876 9.01961
65 5DXI TRE 0.02137 0.40134 9.60265
66 1D1T NAD 0.03664 0.40133 9.65147
67 1U72 NDP 0.02729 0.43797 9.67742
68 1U72 MTX 0.02729 0.43797 9.67742
69 4EBZ NAG NAG NAG NAG 0.01519 0.41933 10.8491
70 4JWH SAH 0.01532 0.41397 13.738
71 4OGN 2U5 0.04177 0.4005 14.2857
72 3O6M PRO LYS LEU GLU PRO TRP LYS HIS PRO 0.0123 0.41769 14.6119
73 1PTR PRB 0.009897 0.40349 22
74 2W9S NDP 0.02517 0.41554 22.9814
Pocket No.: 2; Query (leader) PDB : 3R4S; Ligand: SLB; Similar sites found: 54
This union binding pocket(no: 2) in the query (biounit: 3r4s.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5IE3 AMP 0.02352 0.41715 1.3544
2 5IE3 OXD 0.02352 0.41715 1.3544
3 1V8B NAD 0.007963 0.43638 1.58014
4 4TTB FMN 0.006456 0.42483 1.88679
5 1QG6 NAD 0.01036 0.43274 1.91571
6 1QG6 TCL 0.01036 0.43274 1.91571
7 4RYD 2UE ARG TBG ARG 00S 0.04445 0.40566 2.0316
8 4ZOM 4Q3 0.02558 0.43287 2.22222
9 1T5B FMN 0.0176 0.40275 2.48307
10 2AAZ UMP 0.01641 0.41071 2.52366
11 2PD4 NAD 0.008117 0.42551 2.54545
12 2PD4 DCN 0.01163 0.41468 2.54545
13 4N70 2HX 0.04514 0.40685 2.7439
14 1EQ2 NAP 0.02455 0.40074 2.90323
15 1QRD FAD 0.02829 0.40181 2.9304
16 7CPA FVF 0.0126 0.406 2.9316
17 4LGY ADP 0.02087 0.41273 2.93454
18 4LTN NAI 0.008649 0.44164 3.04569
19 4LTN FMN 0.01035 0.43646 3.04569
20 4PTZ FMN 0.01406 0.42002 3.14136
21 1ICP FMN 0.01676 0.41402 3.19149
22 1Q7E MET 0.006652 0.45855 3.27103
23 1KRH FAD 0.01142 0.41761 3.5503
24 1DMR PGD 0.03737 0.42664 3.61174
25 1V97 MTE 0.04873 0.42088 3.61174
26 3FGC FMN 0.01153 0.42058 3.61446
27 5AMV ADA ADA ADA 0.01767 0.42361 3.7594
28 3OIG NAD 0.01065 0.41643 3.7594
29 2GOU FMN 0.04666 0.40319 3.83562
30 4D42 W0I 0.03696 0.40484 3.90071
31 4D42 NAP 0.03696 0.40484 3.90071
32 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 0.02058 0.4146 4.06504
33 1VYP FMN 0.01403 0.41268 4.12088
34 1VYP TNF 0.01328 0.41268 4.12088
35 3NCQ ATP 0.01689 0.41949 4.20168
36 2OHH FMN 0.01953 0.41421 4.45545
37 2WYV NAD 0.004331 0.45104 4.5977
38 3OOI SAM 0.03116 0.41184 4.74138
39 4J75 TYM 0.003799 0.45154 4.88998
40 3OJF NDP 0.0206 0.40527 5.05837
41 1J3I UMP 0.01355 0.41114 5.35714
42 1A8P FAD 0.0263 0.40523 5.42636
43 3N2S FMN 0.01828 0.40091 5.62249
44 1WWZ ACO 0.03684 0.40104 5.66038
45 1JG0 UMP 0.00613 0.42759 5.68182
46 4ISK UMP 0.009613 0.4235 5.68182
47 2Z9C FMN 0.01516 0.41404 6
48 4R81 FMN 0.0115 0.40094 6.31068
49 3JSX CC2 0.02365 0.429 6.59341
50 3JSX FAD 0.01853 0.42493 6.59341
51 4RDN 6MD 0.004916 0.42009 8.98204
52 2CND FAD 0.01403 0.42647 10
53 1RLJ FMN 0.008876 0.42357 12.2302
54 3RFV 15L 0.03782 0.40011 13.8577
Pocket No.: 3; Query (leader) PDB : 3R4S; Ligand: SLB; Similar sites found: 27
This union binding pocket(no: 3) in the query (biounit: 3r4s.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q8Z NUP 0.003777 0.45052 1.75439
2 2PZM NAD 0.0315 0.41371 1.81818
3 2PZM UDP 0.0315 0.41371 1.81818
4 5H3A D16 0.02267 0.40782 2.4735
5 5H3A UMP 0.01615 0.40782 2.4735
6 4HKP TKW 0.002954 0.46247 2.88462
7 1V35 NAI 0.03423 0.40961 3.03951
8 3ZNN FAD 0.04513 0.4014 3.45821
9 3ZNN 4WL 0.04513 0.4014 3.45821
10 3FSY SCA 0.01682 0.42166 3.61446
11 4EIL UMP 0.0191 0.40493 3.83747
12 3LZW FAD 0.04372 0.42444 3.91566
13 2B3D FAD 0.01397 0.42665 4.41176
14 3QDL FMN 0.008084 0.41998 4.7619
15 1TSD UMP 0.007254 0.43213 5.66038
16 2A9W UMP 0.009844 0.41463 5.68182
17 1ZPR UMP 0.02022 0.40118 5.68182
18 4M5P FMN 0.03687 0.40178 6.14251
19 1DQX BMP 0.002814 0.46182 6.36704
20 1KQB BEZ 0.02226 0.40084 7.37327
21 1KQB FMN 0.02128 0.40009 7.37327
22 1EIX BMQ 0.01568 0.40856 7.7551
23 3IES M24 0.03532 0.41071 9.02935
24 4YEF 4CQ 0.03642 0.40984 11.236
25 1CZR FMN 0.0219 0.40722 11.8343
26 4WB6 ATP 0.03045 0.40015 15
27 5L83 ASP TRP GLU ILE VAL 0.007719 0.41175 15.1786
Pocket No.: 4; Query (leader) PDB : 3R4S; Ligand: SIA; Similar sites found: 14
This union binding pocket(no: 4) in the query (biounit: 3r4s.bio2) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5BUK FAD 0.03851 0.41152 2.48307
2 1XCL SAH 0.04711 0.40124 2.55319
3 2TPS TPS 0.02421 0.40413 3.52423
4 2H21 SAM 0.01817 0.40382 4.77273
5 3IA4 NDP 0.04695 0.40352 5.55556
6 1DAK DPU 0.04531 0.40318 5.80357
7 3LGS SAH 0.02064 0.40315 6.36704
8 3LGS ADE 0.02064 0.40315 6.36704
9 1FDJ 2FP 0.01236 0.40115 6.88705
10 1MJH ATP 0.0125 0.41361 7.40741
11 1MJJ HAL 0.01083 0.41303 7.76256
12 4OR7 NAP 0.04393 0.40285 9.69697
13 5LMK 6ZK 0.01292 0.40434 10.4651
14 4DV8 0LX 0.03893 0.40385 11.0609
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