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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 (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1YXW - TYR GLU TRP n/a n/a
2 3HN1 - SIA SIA n/a n/a
3 1DIW - GAL C6 H12 O6 C([C@@H]1[....
4 5TPC Kd = 0.3 mM GAL SIA NGA GAL SIA n/a n/a
5 2VU9 - GAL BGC GAL SIA NGA SIA n/a n/a
6 3R4S - SLB C11 H19 N O9 CC(=O)N[C@....
7 3OBT - SLB C11 H19 N O9 CC(=O)N[C@....
8 3RSJ - GAL SIA NGA GAL SIA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA; Similar ligands found: 47
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 NGE 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
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 SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 FSI 0.515152 0.895833
17 6KL 0.5 0.807692
18 SFJ 0.5 0.875
19 MN0 0.485714 0.895833
20 EQP 0.470588 0.788462
21 AXP 0.470588 0.788462
22 GAL SIA 0.463415 0.86
23 SID 0.459459 0.82
24 SIA SIA SIA 0.453488 0.826923
25 MUS 0.449438 0.796296
26 NXD 0.447368 0.792453
27 SIA WIA 0.447059 0.767857
28 SIA 2FG 0.447059 0.796296
29 SLT 0.44086 0.877551
30 KDO 0.435484 0.704545
31 SIA GAL 0.435294 0.86
32 SIA NAG 0.430233 0.781818
33 4U0 0.427083 0.86
34 4U2 0.425532 0.843137
35 BND 0.416667 0.807692
36 SKD 0.414286 0.875
37 SIA SIA GAL 0.410526 0.811321
38 4U1 0.408163 0.826923
39 E3M 0.402778 0.606061
40 SIA GAL GLC 0.402062 0.86
41 BGC SIA GAL 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 BGC GAL SIA 0.402062 0.86
44 SIA GAL BGC 0.402062 0.86
45 GLA GLC SIA 0.402062 0.86
46 4AM 0.4 0.833333
47 DAN 0.4 0.911111
Ligand no: 2; Ligand: SLB; Similar ligands found: 47
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 NGE 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
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 SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 FSI 0.515152 0.895833
17 6KL 0.5 0.807692
18 SFJ 0.5 0.875
19 MN0 0.485714 0.895833
20 EQP 0.470588 0.788462
21 AXP 0.470588 0.788462
22 GAL SIA 0.463415 0.86
23 SID 0.459459 0.82
24 SIA SIA SIA 0.453488 0.826923
25 MUS 0.449438 0.796296
26 NXD 0.447368 0.792453
27 SIA WIA 0.447059 0.767857
28 SIA 2FG 0.447059 0.796296
29 SLT 0.44086 0.877551
30 KDO 0.435484 0.704545
31 SIA GAL 0.435294 0.86
32 SIA NAG 0.430233 0.781818
33 4U0 0.427083 0.86
34 4U2 0.425532 0.843137
35 BND 0.416667 0.807692
36 SKD 0.414286 0.875
37 SIA SIA GAL 0.410526 0.811321
38 4U1 0.408163 0.826923
39 E3M 0.402778 0.606061
40 SIA GAL GLC 0.402062 0.86
41 BGC SIA GAL 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 BGC GAL SIA 0.402062 0.86
44 SIA GAL BGC 0.402062 0.86
45 GLA GLC SIA 0.402062 0.86
46 4AM 0.4 0.833333
47 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 with APoc: 121
This union binding pocket(no: 1) in the query (biounit: 3r4s.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3C1X CKK 1.34048
2 5I60 67W 1.35501
3 5MZI FAD 1.58014
4 5MZI FYK 1.58014
5 4L80 1VU 1.72414
6 4YDQ HFG 1.80587
7 4YDQ ANP 1.80587
8 1IXE COA 1.85676
9 2BLN U5P 1.96721
10 2BLN FON 1.96721
11 5JFL NAD 2.0316
12 3HGM ATP 2.04082
13 1ZVW PRP 2.1164
14 1TIW FAD 2.25734
15 1TIW TFB 2.25734
16 4O8A FAD 2.25734
17 5KF6 FAD 2.25734
18 5KF6 TFB 2.25734
19 3FXU TSU 2.29508
20 4XCZ T3Q 2.39808
21 4XCZ FON 2.39808
22 1VA6 P2S 2.48307
23 1VA6 ADP 2.48307
24 3HAZ FAD 2.48307
25 2WZV FMN 2.55319
26 2QBU SAH 2.58621
27 5D4V SAH 2.61194
28 3BEO UD1 2.66667
29 1TV5 FMN 2.7088
30 5O2N NAG 2.7088
31 3DCJ THH 2.7907
32 1GAR U89 2.83019
33 2E1T MLC 2.93454
34 5UIJ TYD 2.96296
35 5GS9 ARG 2.96736
36 5YAK FMN 3.0303
37 5VYR B62 3.06513
38 5VYR GMP 3.06513
39 5DX9 T6P 3.16456
40 1GSA ADP 3.16456
41 1QPR PPC 3.16901
42 2AKO ADP 3.18725
43 5BV3 M7G 3.18841
44 5O1I 9GH 3.19635
45 4GLW NMN 3.27869
46 5Y80 IRE 3.37838
47 1EC9 XYH 3.386
48 4ANP 3QI 3.39506
49 3OZ2 OZ2 3.52645
50 4LXQ TYD 3.64964
51 4LXQ FON 3.64964
52 4KWI NAP 3.80228
53 4KWI 1TJ 3.80228
54 4FFG LBS 3.83747
55 5HDJ FMN 3.89105
56 2X00 GYN 3.96476
57 2Q7V FAD 4
58 3AB4 THR 4.038
59 3BC9 ACR 4.06321
60 3LL9 ADP 4.08922
61 3HMO STU 4.09357
62 2DT9 THR 4.19162
63 4DHY S41 4.28894
64 4WOP CTP 4.44444
65 3KRL KRL 4.77612
66 4UCI ADN 4.81928
67 4L2I NAD 4.94297
68 4L2I FAD 4.94297
69 4JWJ SAH 4.9505
70 2V95 HCY 5.12129
71 2J4K U5P 5.30973
72 2FNA ADP 5.32213
73 2FV5 541 5.36398
74 3ZRM ZRM 5.39084
75 2VAP GDP 5.49451
76 3BNK FMN 5.61225
77 3N2S FMN 5.62249
78 5OO5 UUA 5.64516
79 1TLC DGP 5.66038
80 2YC5 6BC 5.70175
81 4Y8D 49J 5.71429
82 4GV8 DUP 5.91716
83 1USF NAP 6.17978
84 1USF FMN 6.17978
85 1GTE IUR 6.32054
86 1GTE FMN 6.32054
87 1I52 CTP 6.35593
88 1DQX BMP 6.36704
89 4ZX2 4TE 6.60661
90 1RC0 KT5 6.69856
91 5L01 6Z4 6.77201
92 3MYZ TFX 7
93 5DS8 GLY 5CT GLY ALA 7.20721
94 1P9P SAH 7.27969
95 1MJH ATP 7.40741
96 4B7X NAP 7.44048
97 4R2M ANP 7.59494
98 1MJJ HAL 7.76256
99 4XDA ADP 7.76699
100 3G5S FAD 7.90068
101 5MVR ADP 8.02469
102 4FN4 NAD 8.26772
103 4MO4 ACP 8.35579
104 4X7Y SAH 8.75912
105 5VYQ FON 9.01961
106 4YFY 1YJ 9.02935
107 6CAY ERG 9.46746
108 5DXI TRE 9.60265
109 1D1T NAD 9.65147
110 1U72 MTX 9.67742
111 1U72 NDP 9.67742
112 5J6D 6H5 9.77199
113 5CUO COA 9.90099
114 6EDK 1YA 10.1382
115 4EBZ NAG NAG NAG NAG 10.8491
116 6CWH 6LA 12.0879
117 4JWH SAH 13.738
118 4OGN 2U5 14.2857
119 3O6M PRO LYS LEU GLU PRO TRP LYS HIS PRO 14.6119
120 2V17 THR ASP HIS GLY ALA GLU 14.9533
121 2W9S NDP 22.9814
Pocket No.: 2; Query (leader) PDB : 3R4S; Ligand: SLB; Similar sites found with APoc: 83
This union binding pocket(no: 2) in the query (biounit: 3r4s.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 5IE3 AMP 1.3544
2 5IE3 OXD 1.3544
3 1V8B NAD 1.58014
4 5DF1 58X 1.63043
5 5DF1 NAP 1.63043
6 4RYD 2UE ARG TBG ARG 00S 2.0316
7 2R14 TXD 2.38727
8 1T5B FMN 2.48307
9 5LMC FMN 2.48307
10 5NTP 98E 2.52101
11 2AAZ UMP 2.52366
12 2PD4 DCN 2.54545
13 2PD4 NAD 2.54545
14 4N70 2HX 2.7439
15 1EQ2 NAP 2.90323
16 1QRD FAD 2.9304
17 7CPA FVF 2.9316
18 4LGY ADP 2.93454
19 5YAK FMN 3.0303
20 4LTN NAI 3.04569
21 4LTN FMN 3.04569
22 5MJI 7O6 3.11284
23 4PTZ FMN 3.14136
24 3DLG GWE 3.18182
25 1ICP FMN 3.19149
26 1Q7E MET 3.27103
27 5AE9 OKO 3.386
28 1KRH FAD 3.5503
29 1DMR PGD 3.61174
30 1V97 MTE 3.61174
31 3FGC FMN 3.61446
32 3L9W FMN 3.63196
33 5AMV ADA ADA ADA 3.7594
34 3OIG NAD 3.7594
35 2GOU FMN 3.83562
36 4EIL UMP 3.83747
37 6A1G 9OL 3.88889
38 4D42 W0I 3.90071
39 4D42 NAP 3.90071
40 3OYZ ACO 3.9261
41 3LL2 MAN MAN MAN MAN MAN MAN MAN MAN 4.06504
42 1VYP TNF 4.12088
43 3NCQ ATP 4.20168
44 4D62 SIA 4.27807
45 6FRN FMN 4.39024
46 2B3D FAD 4.41176
47 2OHH FMN 4.45545
48 5EYG NAP 4.5283
49 2WYV NAD 4.5977
50 1T0I FMN 4.71204
51 3AKI AH8 4.74041
52 6MB9 COA 4.74453
53 4J75 TYM 4.88998
54 3OJF IMJ 5.05837
55 3OJF NDP 5.05837
56 1J3I UMP 5.35714
57 1A8P FAD 5.42636
58 3N2S FMN 5.62249
59 4CU1 71S 5.64334
60 1WWZ ACO 5.66038
61 1JG0 UMP 5.68182
62 4ISK UMP 5.68182
63 1NCE UMP 5.68182
64 6CDZ UMC 5.70342
65 6CDZ UMP 5.70342
66 1YRX FMN 5.78512
67 5UGH 8AJ 5.79345
68 2YYY NAP 5.8309
69 2Z9C FMN 6
70 2Z9C DTC 6
71 4R81 FMN 6.31068
72 3JSX CC2 6.59341
73 3JSX FAD 6.59341
74 3IO3 ADP 7.18391
75 3B2Q AES 8.35214
76 4RDN 6MD 8.98204
77 5AHS FAD 9.22693
78 5ANU 58T 9.49367
79 2CND FAD 10
80 4QVB F42 10.2041
81 1RLJ FMN 12.2302
82 3RFV 15L 13.8577
83 4S1D 41M 14.9533
Pocket No.: 3; Query (leader) PDB : 3R4S; Ligand: SLB; Similar sites found with APoc: 39
This union binding pocket(no: 3) in the query (biounit: 3r4s.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5CG1 NAD BBN 1.63934
2 2Q8Z NUP 1.75439
3 2PZM UDP 1.81818
4 2PZM NAD 1.81818
5 1QG6 NAD 1.91571
6 1QG6 TCL 1.91571
7 3FXU TSU 2.29508
8 5H3A D16 2.4735
9 5H3A UMP 2.4735
10 4HKP TKW 2.88462
11 1V35 NAI 3.03951
12 4Q9N NAI 3.3557
13 3ZNN 4WL 3.45821
14 3ZNN FAD 3.45821
15 5WAN FMN 3.47395
16 3FSY SCA 3.61446
17 3QDL FMN 4.7619
18 6EJI UD2 5.09383
19 3MQG ACO 5.20833
20 1TSD UMP 5.66038
21 2A9W UMP 5.68182
22 1ZPR UMP 5.68182
23 3WMX NAD 6.09481
24 4M5P FMN 6.14251
25 1DQX BMP 6.36704
26 1KQB BEZ 7.37327
27 1KQB FMN 7.37327
28 1EIX BMQ 7.7551
29 3IES M24 9.02935
30 6ASZ GLN THR ALA ARG M3L SER 10.1449
31 1CZR FMN 11.8343
32 2WUF KEM 12.0275
33 4WB6 ATP 15
34 5L83 ASP TRP GLU ILE VAL 15.1786
35 4U8P FDA 17.1558
36 4U8P UDP 17.1558
37 5WHU SIA GAL 20.1342
38 1NNU NAD 25
39 1NNU TCT 25
Pocket No.: 4; Query (leader) PDB : 3R4S; Ligand: SIA; Similar sites found with APoc: 18
This union binding pocket(no: 4) in the query (biounit: 3r4s.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4CW5 FMN 2.0316
2 5BUK FAD 2.48307
3 1XCL SAH 2.55319
4 1UP7 NAD 2.8777
5 2TPS TPS 3.52423
6 5AVF TAU 3.89105
7 2H21 SAM 4.77273
8 3IA4 NDP 5.55556
9 1DAK DPU 5.80357
10 1DAK ADP 5.80357
11 3LGS SAH 6.36704
12 3LGS ADE 6.36704
13 3NUG NAD 6.47773
14 1FDJ 2FP 6.88705
15 4OR7 NAP 9.69697
16 5LMK 6ZK 10.4651
17 4DV8 0LX 11.0609
18 5ZFJ 9BF 14.0969
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