Receptor
PDB id Resolution Class Description Source Keywords
3EFX 1.94 Å NON-ENZYME: TOXIN_VIRAL NOVEL BINDING SITE IDENTIFIED IN A HYBRID BETWEEN CHOLERA TO HEAT-LABILE ENTEROTOXIN, 1.9A CRYSTAL STRUCTURE REVEALS THE VIBRIO CHOLERAE PROTEIN-CARBOHYDRATE COMPLEX CHOLERA TOXIN HEAT-LABILE ENTBLOOD GROUP ANTIGEN TOXIN
Ref.: NOVEL BINDING SITE IDENTIFIED IN A HYBRID BETWEEN C TOXIN AND HEAT-LABILE ENTEROTOXIN: 1.9 A CRYSTAL ST REVEALS THE DETAILS STRUCTURE V. 12 1655 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BGC FUC GAL FUC A2G B:1;
T:1;
A:1;
C:1;
N:1;
Q:1;
S:1;
O:1;
R:1;
P:1;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
837.775 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MD2 1.45 Å NON-ENZYME: TOXIN_VIRAL CHOLERA TOXIN B-PENTAMER WITH DECAVALENT LIGAND BMSC-0013 VIBRIO CHOLERAE MULTIVALENT INHIBITOR TOXIN TOXIN
Ref.: SOLUTION AND CRYSTALLOGRAPHIC STUDIES OF BRANCHED MULTIVALENT LIGANDS THAT INHIBIT THE RECEPTOR-BINDI CHOLERA TOXIN. J.AM.CHEM.SOC. V. 124 12991 2002
Members (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 64 families.
1 5LZJ - 7BT C20 H29 N O9 COc1cc(cc(....
2 5ELB Kd = 1.1 mM GAL NDG FUC FUC n/a n/a
3 1JR0 Kd = 12 uM A24 C19 H27 N3 O10 c1c(cc(cc1....
4 6HJD Kd = 10 mM NDG FUC GAL n/a n/a
5 5ELE - NDG GAL FUC A2G FUC n/a n/a
6 3EFX - BGC FUC GAL FUC A2G n/a n/a
7 1RF2 ic50 = 17 uM BV4 C79 H123 N15 O32 c1c(cc(cc1....
8 5ELD Kd = 2.19 mM NDG GAL FUC A2G FUC n/a n/a
9 1PZJ ic50 = 0.32 mM 15B C23 H37 N5 O9 c1c(cc(cc1....
10 1G8Z - GAL C6 H12 O6 C([C@@H]1[....
11 1CT1 - BGC GAL SIA NGA GAL n/a n/a
12 5LZG - 7BN C24 H39 N5 O14 CC(=O)N[C@....
13 5ELF Kd = 4.57 mM BGC FUC GAL FUC A2G n/a n/a
14 1LLR - FNG LNQ n/a n/a
15 1RCV ic50 = 29 uM BV1 C50 H72 N10 O20 c1c(cc(cc1....
16 6HMW - FUL C6 H12 O5 C[C@H]1[C@....
17 1MD2 Kd ~ 40 nM 233 C14 H26 N2 O8 COC(=O)NCC....
18 1PZK ic50 = 0.2 mM J12 C29 H43 N5 O8 S c1cc(sc1)C....
19 1RDP ic50 = 9 uM BV3 C63 H91 N15 O26 c1c(cc(cc1....
20 1RD9 ic50 = 13 uM BV2 C51 H79 N11 O22 c1c(cc(cc1....
21 3CHB - BGC GAL SIA NGA GAL n/a n/a
22 1EEI ic50 = 0.7 mM GAA C12 H15 N O8 c1cc(cc(c1....
23 2CHB - GAL SIA NGA GAL n/a n/a
24 6HMY - FUC C6 H12 O5 C[C@H]1[C@....
25 5ELC Kd = 1.5 mM GAL NAG FUC FUC n/a n/a
70% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 1DJR - GLA BEZ n/a n/a
2 1FD7 ic50 = 14 mM AI1 C20 H23 N O7 c1ccc(cc1)....
3 2XRS - GAL NAG GAL n/a n/a
4 1EFI ic50 = 12 mM GAT C12 H17 N O6 c1cc(ccc1N....
5 1JQY Ki = 12 uM A32 C20 H29 N3 O10 c1c(cc(cc1....
6 1PZI Kd = 60 uM 1DM C24 H36 N4 O11 c1c(cc(cc1....
7 2XRQ - BGC GAL SIA NGA GAL n/a n/a
8 1EEF ic50 = 1.2 mM GLA C6 H12 O6 C([C@@H]1[....
9 6IAL Kd = 5 mM BGC GAL NAG NAG GAL GAL n/a n/a
10 1LT6 - GAA C12 H15 N O8 c1cc(cc(c1....
11 5LZI - 7BQ C32 H46 N6 O15 CC(=O)N[C@....
12 1LT5 - YIO GAL n/a n/a
13 5LZJ - 7BT C20 H29 N O9 COc1cc(cc(....
14 5ELB Kd = 1.1 mM GAL NDG FUC FUC n/a n/a
15 1JR0 Kd = 12 uM A24 C19 H27 N3 O10 c1c(cc(cc1....
16 6HJD Kd = 10 mM NDG FUC GAL n/a n/a
17 5ELE - NDG GAL FUC A2G FUC n/a n/a
18 3EFX - BGC FUC GAL FUC A2G n/a n/a
19 1RF2 ic50 = 17 uM BV4 C79 H123 N15 O32 c1c(cc(cc1....
20 5ELD Kd = 2.19 mM NDG GAL FUC A2G FUC n/a n/a
21 1PZJ ic50 = 0.32 mM 15B C23 H37 N5 O9 c1c(cc(cc1....
22 1G8Z - GAL C6 H12 O6 C([C@@H]1[....
23 1CT1 - BGC GAL SIA NGA GAL n/a n/a
24 5LZG - 7BN C24 H39 N5 O14 CC(=O)N[C@....
25 5ELF Kd = 4.57 mM BGC FUC GAL FUC A2G n/a n/a
26 1LLR - FNG LNQ n/a n/a
27 1RCV ic50 = 29 uM BV1 C50 H72 N10 O20 c1c(cc(cc1....
28 6HMW - FUL C6 H12 O5 C[C@H]1[C@....
29 1MD2 Kd ~ 40 nM 233 C14 H26 N2 O8 COC(=O)NCC....
30 1PZK ic50 = 0.2 mM J12 C29 H43 N5 O8 S c1cc(sc1)C....
31 1RDP ic50 = 9 uM BV3 C63 H91 N15 O26 c1c(cc(cc1....
32 1RD9 ic50 = 13 uM BV2 C51 H79 N11 O22 c1c(cc(cc1....
33 3CHB - BGC GAL SIA NGA GAL n/a n/a
34 1EEI ic50 = 0.7 mM GAA C12 H15 N O8 c1cc(cc(c1....
35 2CHB - GAL SIA NGA GAL n/a n/a
36 6HMY - FUC C6 H12 O5 C[C@H]1[C@....
37 5ELC Kd = 1.5 mM GAL NAG FUC FUC n/a n/a
50% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 1DJR - GLA BEZ n/a n/a
2 1FD7 ic50 = 14 mM AI1 C20 H23 N O7 c1ccc(cc1)....
3 2XRS - GAL NAG GAL n/a n/a
4 1EFI ic50 = 12 mM GAT C12 H17 N O6 c1cc(ccc1N....
5 1JQY Ki = 12 uM A32 C20 H29 N3 O10 c1c(cc(cc1....
6 1PZI Kd = 60 uM 1DM C24 H36 N4 O11 c1c(cc(cc1....
7 2XRQ - BGC GAL SIA NGA GAL n/a n/a
8 1EEF ic50 = 1.2 mM GLA C6 H12 O6 C([C@@H]1[....
9 6IAL Kd = 5 mM BGC GAL NAG NAG GAL GAL n/a n/a
10 1LT6 - GAA C12 H15 N O8 c1cc(cc(c1....
11 5LZI - 7BQ C32 H46 N6 O15 CC(=O)N[C@....
12 1LT5 - YIO GAL n/a n/a
13 5LZJ - 7BT C20 H29 N O9 COc1cc(cc(....
14 5ELB Kd = 1.1 mM GAL NDG FUC FUC n/a n/a
15 1JR0 Kd = 12 uM A24 C19 H27 N3 O10 c1c(cc(cc1....
16 6HJD Kd = 10 mM NDG FUC GAL n/a n/a
17 5ELE - NDG GAL FUC A2G FUC n/a n/a
18 3EFX - BGC FUC GAL FUC A2G n/a n/a
19 1RF2 ic50 = 17 uM BV4 C79 H123 N15 O32 c1c(cc(cc1....
20 5ELD Kd = 2.19 mM NDG GAL FUC A2G FUC n/a n/a
21 1PZJ ic50 = 0.32 mM 15B C23 H37 N5 O9 c1c(cc(cc1....
22 1G8Z - GAL C6 H12 O6 C([C@@H]1[....
23 1CT1 - BGC GAL SIA NGA GAL n/a n/a
24 5LZG - 7BN C24 H39 N5 O14 CC(=O)N[C@....
25 5ELF Kd = 4.57 mM BGC FUC GAL FUC A2G n/a n/a
26 1LLR - FNG LNQ n/a n/a
27 1RCV ic50 = 29 uM BV1 C50 H72 N10 O20 c1c(cc(cc1....
28 6HMW - FUL C6 H12 O5 C[C@H]1[C@....
29 1MD2 Kd ~ 40 nM 233 C14 H26 N2 O8 COC(=O)NCC....
30 1PZK ic50 = 0.2 mM J12 C29 H43 N5 O8 S c1cc(sc1)C....
31 1RDP ic50 = 9 uM BV3 C63 H91 N15 O26 c1c(cc(cc1....
32 1RD9 ic50 = 13 uM BV2 C51 H79 N11 O22 c1c(cc(cc1....
33 3CHB - BGC GAL SIA NGA GAL n/a n/a
34 1EEI ic50 = 0.7 mM GAA C12 H15 N O8 c1cc(cc(c1....
35 2CHB - GAL SIA NGA GAL n/a n/a
36 6HMY - FUC C6 H12 O5 C[C@H]1[C@....
37 5ELC Kd = 1.5 mM GAL NAG FUC FUC n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC FUC GAL FUC A2G; Similar ligands found: 104
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC FUC GAL FUC A2G 1 1
2 NAG FUC GAL FUC A2G 0.8 0.959184
3 BGC GAL FUC A2G 0.797619 0.978723
4 NAG GAL FUC FUC A2G 0.77907 0.959184
5 BGC FUC GAL NAG 0.77381 0.978723
6 GLC GAL NAG GAL FUC A2G 0.690722 0.959184
7 GAL FUC A2G 0.682927 0.978723
8 BGC FUC GAL NAG GAL 0.631579 0.978723
9 HSH A2G FUC 0.630435 0.854545
10 NAG GAL FUC GLA 0.622222 0.978723
11 GLC GAL NAG GAL FUC GLA 0.606061 0.978723
12 BGC FUC GAL 0.6 0.723404
13 GLC BGC FUC GAL 0.6 0.723404
14 BGC GAL FUC GLA 0.586207 0.723404
15 GLA NAG GAL FUC 0.55914 0.978723
16 GAL NGA A2G 0.54023 0.938776
17 NDG FUC GAL FUC 0.538462 1
18 GAL NAG GAL FUC FUC 0.536082 1
19 BGC GAL NGA 0.534091 0.957447
20 BMA MAN NAG 0.533333 0.957447
21 GAL NAG FUC GAL 0.526316 0.978723
22 NAG GAL FUC FUC 0.521739 1
23 BGC GAL GLA NGA 0.515789 0.957447
24 NDG GLA NAG GLC RAM 0.513761 0.959184
25 NDG NAG GLA NAG GLC RAM 0.513761 0.959184
26 NAG FUC GAL 0.511111 0.978723
27 BGC GAL NAG 0.51087 0.957447
28 BGC GAL NAG GAL FUC 0.509804 0.978723
29 NAG GAL FUC A2G 0.505495 0.978723
30 NDG GLA GLC NAG GLC RAM 0.5 0.959184
31 NAG GAL FUC 0.5 0.978723
32 GAL NAG GAL FUC 0.494949 0.938776
33 BGC GAL NAG GAL FUC FUC 0.490566 1
34 MAG FUC GAL FUC 0.489362 0.979167
35 A2G NAG 0.488372 0.938776
36 GDL NAG 0.488372 0.938776
37 MAN MAN MAN NAG NAG 0.484848 0.938776
38 MBG A2G 0.482759 0.958333
39 MAN NAG 0.482353 0.957447
40 MAN MAN NAG 0.478723 0.918367
41 NAG GAL NAG 0.478723 0.938776
42 GAL NGA 0.477273 0.897959
43 GAL FUC GAL 0.476744 0.723404
44 NAG FUC 0.476744 0.957447
45 MAG GAL FUC FUC 0.473684 0.979167
46 MMA MAN NAG 0.473118 0.958333
47 MBG NAG 0.471264 0.958333
48 AMU NAG 0.46875 0.94
49 BMA MAN MAN NAG GAL NAG 0.46789 0.938776
50 NAG NAG NAG NAG NAG NAG NAG NAG 0.466667 0.959184
51 NDG NAG NAG NAG NAG 0.466667 0.959184
52 NAG NAG NAG NAG NAG NAG 0.466667 0.959184
53 NAG NAG NAG NAG NAG 0.466667 0.959184
54 NAG NAG BMA MAN NAG 0.461538 0.959184
55 BGC GAL FUC 0.460674 0.723404
56 GLC GAL BGC FUC 0.460674 0.723404
57 GAL NAG GAL 0.457447 0.957447
58 3QL 0.451613 0.867925
59 MAG SGA FUC 0.45098 0.71875
60 GAL NAG GAL NAG GAL 0.44898 0.938776
61 BGC GAL NGA GAL 0.447917 0.957447
62 GLA NAG FUC GAL 0.446602 0.958333
63 NDG NAG 0.444444 0.959184
64 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.444444 0.94
65 NAG BDP NAG BDP NAG BDP NAG 0.442308 0.94
66 HSH GLA FUC 0.4375 0.636364
67 NM9 NAG 0.43299 0.921569
68 NAG NAG NAG NAG 0.43299 0.886792
69 NAG NAG NAG 0.43299 0.886792
70 NAG NAG NAG NAG NAG NAG NAG 0.43299 0.886792
71 Z4S NAG NAG 0.43 0.886792
72 NAG GAL GLC NAG GLC RAM 0.427184 0.938776
73 RAM MAN GLA TYV RAM GLC MAN GLA TYV 0.424779 0.734694
74 BGC GAL NAG GAL 0.424242 0.957447
75 AH0 NAG 0.424242 0.87037
76 NAG NGO 0.42268 0.851852
77 BGC GAL GLA NGA GAL 0.421569 0.957447
78 MMA MAN NAG MAN NAG NAG 0.419048 0.94
79 RAM MAN GLA ABE 0.417476 0.714286
80 BMA Z4Y NAG 0.417476 0.9375
81 GAL SIA NGA 0.417391 0.903846
82 NAG NON FUC GAL FUC 0.414414 0.854545
83 MAG FUC SGA 0.409524 0.707692
84 C4W NAG FUC BMA MAN MAN NAG NAG 0.409449 0.903846
85 NDG BMA MAN MAN NAG GAL NAG 0.40678 0.959184
86 NDG GAL FUC FUC 0.405941 0.92
87 NAG GAL NAG GAL NAG GAL 0.405941 0.959184
88 NAG GAL NAG GAL 0.405941 0.938776
89 AMU ALA NAG DGL 0.405172 0.87037
90 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.40458 0.810345
91 LEC NGA 0.403846 0.734375
92 NAG AH0 0.403846 0.87037
93 NDG BMA MAN MAN NAG MAN MAN 0.403361 0.938776
94 NAG NAG BMA MAN MAN NAG GAL NAG 0.403361 0.959184
95 MAG 0.402439 0.895833
96 2F8 0.402439 0.895833
97 GAL NAG 0.402174 0.957447
98 MAN NAG GAL 0.402062 0.957447
99 NAG NOJ NAG 0.401961 0.821429
100 NAG NOJ NAG NAG 0.401961 0.839286
101 MUB ALA NAG ZGL 0.401709 0.854545
102 GAL FUC NGA 0.4 0.9
103 YZ0 MAN MAN NAG MAN 0.4 0.958333
104 NGT NAG 0.4 0.810345
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC FUC GAL FUC A2G; Similar ligands found: 4
No: Ligand Similarity coefficient
1 GLC GAL FUC A2G FUC 0.9689
2 BGC GAL FUC A2G FUC 0.9582
3 NDG GAL FUC A2G FUC 0.9370
4 GLC FUC GAL FUC A2G 0.9270
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MD2; Ligand: 233; 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: 1md2.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
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