Receptor
PDB id Resolution Class Description Source Keywords
3OBT 2 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE D LIGAND DOMAIN IN COMPLEX WITH N-ACETYLNEURAMINIC ACID CLOSTRIDIUM BOTULINUM NEUROTOXIN GANGALIOSIDE HYDROLASE
Ref.: BOTULINUM NEUROTOXIN SEROTYPE D ATTACKS NEURONS VIA CARBOHYDRATE-BINDING SITES IN A GANGLIOSIDE-DEPENDE MANNER. BIOCHEM.J. V. 431 207 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:10;
A:11;
A:12;
A:2;
A:3;
A:4;
A:5;
A:6;
A:7;
A:8;
A:9;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SLB A:1;
Valid;
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
3OBT 2 Å EC: 3.4.24.69 CRYSTAL STRUCTURE OF BOTULINUM NEUROTOXIN SEROTYPE D LIGAND DOMAIN IN COMPLEX WITH N-ACETYLNEURAMINIC ACID CLOSTRIDIUM BOTULINUM NEUROTOXIN GANGALIOSIDE HYDROLASE
Ref.: BOTULINUM NEUROTOXIN SEROTYPE D ATTACKS NEURONS VIA CARBOHYDRATE-BINDING SITES IN A GANGLIOSIDE-DEPENDE MANNER. BIOCHEM.J. V. 431 207 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3OBT - 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 3OBT - 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: 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 : 3OBT; Ligand: SLB; Similar sites found: 114
This union binding pocket(no: 1) in the query (biounit: 3obt.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FWP CIT 0.004644 0.45004 None
2 2FWP ICR 0.01195 0.41467 None
3 1UAS GLA 0.009319 0.43277 1.10497
4 1EZ0 NAP 0.027 0.40947 1.6129
5 4LZJ 22H 0.01891 0.4034 1.65016
6 2C6Q NDP 0.0235 0.41953 1.7094
7 2BO4 FLC 0.03495 0.42261 1.76322
8 3A23 GAL 0.007711 0.4375 1.84332
9 2E5V FAD 0.02583 0.40239 1.84332
10 3EYA FAD 0.02202 0.40048 1.84332
11 3RKR NAP 0.02091 0.40366 1.9084
12 4JD3 COA 0.01608 0.40125 1.983
13 4JD3 PLM 0.01658 0.40125 1.983
14 1KOL NAD 0.004309 0.45166 2.01005
15 3PC3 P1T 0.0009648 0.47754 2.07373
16 1DY4 SNP 0.04957 0.41738 2.07373
17 4Y85 499 0.01743 0.40905 2.10843
18 3ETG GTP 0.03855 0.44236 2.30415
19 1UZN NAP 0.02837 0.40907 2.42915
20 1A5Z NAD 0.03009 0.4158 2.50784
21 3N1S 5GP 0.004705 0.42146 2.52101
22 1UCD U5P 0.004503 0.41072 2.63158
23 2XVD AS6 0.03333 0.4007 2.64901
24 2QQ0 THM 0.004032 0.43911 2.71739
25 2QQ0 ANP 0.004438 0.43911 2.71739
26 2QQ0 TMP 0.004786 0.43639 2.71739
27 1QM5 PLP 0.02277 0.42233 2.76498
28 1QM5 GLC GLC GLC PO4 SGC GLC 0.01185 0.41916 2.76498
29 2G5C NAD 0.02656 0.40375 2.84698
30 1X7D ORN 0.009418 0.44888 2.85714
31 1X7D NAD 0.007144 0.44625 2.85714
32 3GGO NAI 0.04294 0.41666 2.86624
33 3GGO ENO 0.04294 0.41666 2.86624
34 2O4C NAD 0.03512 0.41258 2.89474
35 3GGF GVD 0.005816 0.40198 2.99003
36 3LL5 ATP 0.008677 0.43835 3.21285
37 2WPF WPF 0.001376 0.49135 3.22581
38 2WPF FAD 0.001929 0.47667 3.22581
39 2GTE VA 0.01825 0.40103 3.22581
40 1WPQ NAD 0.01925 0.40695 3.4384
41 3QVP FAD 0.004786 0.45793 3.45622
42 3NRR UMP 0.005556 0.44431 3.45622
43 3MB5 SAM 0.03426 0.40727 3.52941
44 2VFT SOR 0.003244 0.42395 3.5545
45 5W4W 9WG 0.01991 0.41195 3.62538
46 1R27 MGD 0.049 0.40334 3.68664
47 1H74 ILE 0.03557 0.40192 3.71622
48 1H74 ADP 0.0384 0.40192 3.71622
49 2KCE D16 0.01283 0.42846 3.78788
50 1XHC FAD 0.04876 0.40658 3.81471
51 2OEG UPG 0.003418 0.41802 3.91705
52 4D1J DGJ 0.004902 0.41095 3.91705
53 4QAR ADE 0.008426 0.40751 3.9801
54 3M2W L8I 0.005431 0.42423 4.01338
55 2YX1 SFG 0.01047 0.42545 4.16667
56 3CIF NAD 0.02972 0.42378 4.17827
57 2CSN CKI 0.004225 0.41634 4.3771
58 2RAB FAD 0.03359 0.42637 4.37788
59 4ANW O92 0.005358 0.42183 4.60829
60 3OND ADN 0.0353 0.41798 4.60829
61 3OND NAD 0.0353 0.41798 4.60829
62 2B4R NAD 0.03194 0.42182 4.63768
63 3ZLM ANP 0.006766 0.43302 4.78723
64 2XVF FAD 0.04137 0.42487 4.83871
65 3VPC ADP 0.01325 0.42831 4.96454
66 1YKD CMP 0.00684 0.42062 5.02513
67 3U2U UDP 0.03153 0.40215 5.32319
68 4JR7 GNP 0.004946 0.40307 5.34759
69 2D3S TNR 0.0238 0.40118 5.3719
70 5BSH PRO 0.02162 0.41322 5.41516
71 4BQO COA 0.009142 0.40734 5.44872
72 2DFV NAD 0.006774 0.43143 5.4755
73 3SE5 ANP 0.006485 0.43014 5.4878
74 1OTH PAO 0.01403 0.40111 5.919
75 1NV8 SAM 0.0207 0.42961 5.98592
76 1NV8 MEQ 0.02004 0.4284 5.98592
77 2Q28 ADP 0.02484 0.41519 5.99078
78 2EJU SAH 0.0357 0.40001 6.08466
79 2Y4N DLL 0.01141 0.42236 6.45161
80 3OJO NAD 0.04218 0.40014 6.49652
81 3V1Y NAD 0.02911 0.4206 6.52819
82 4JK3 NAD 0.02124 0.40893 6.56371
83 3WGT QSC 0.04088 0.40787 6.62824
84 3WGT FAD 0.03987 0.40787 6.62824
85 3KLJ FAD 0.02253 0.41748 6.75325
86 4GID 0GH 0.04488 0.40703 6.95876
87 2WR9 MAN MAN 0.00988 0.41785 7.03125
88 1T3Q MCN 0.02042 0.41378 7.14286
89 3LXN MI1 0.01619 0.40062 7.2327
90 2ZKJ ADP 0.0446 0.41005 7.36041
91 2Q97 ATP 0.01113 0.42981 7.75194
92 2X2M X2M 0.01458 0.4021 7.96178
93 1L3I SAH 0.009305 0.45585 8.33333
94 3V91 UPG 0.01872 0.41084 8.59107
95 1UR4 B2G 0.02384 0.43012 9.27318
96 3VC3 C6P 0.01553 0.42879 9.30233
97 3Q9N COA 0.03571 0.40287 9.49367
98 5NTW 98N 0.01939 0.42281 9.72763
99 2FVV IHP 0.03895 0.40235 9.79381
100 3VMW ADA ADA ADA 0.006159 0.4049 9.81595
101 3RNM FAD 0.02591 0.41047 10.3448
102 3SXF BK5 0.01966 0.43329 10.8295
103 2BME GNP 0.01336 0.4105 11.2903
104 2FXV 5GP 0.02819 0.40436 11.3402
105 1B4U DHB 0.0007278 0.44323 12.9496
106 1O9W NAG 0.005728 0.4278 14.1243
107 3AD8 NAD 0.02235 0.41119 14.1414
108 5CSD ACD 0.01733 0.40112 15.0943
109 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.01108 0.42218 15.1786
110 5BTX CMP 0.003544 0.40871 17.1233
111 4II2 ATP 0.01136 0.43152 21.6867
112 2F5Z FAD 0.01613 0.43487 21.875
113 1R18 SAH 0.01126 0.41212 22.0264
114 3Q87 SAM 0.006429 0.41954 27.2
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