Receptor
PDB id Resolution Class Description Source Keywords
2CHB 2 Å NON-ENZYME: TOXIN_VIRAL CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE VIBRIO CHOLERAE TOXIN-RECEPTOR COMPLEX PENTASACCHARIDE TOXIN
Ref.: STRUCTURAL STUDIES OF RECEPTOR BINDING BY CHOLERA T MUTANTS. PROTEIN SCI. V. 6 1516 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GAL NGA GAL SIA A:1;
 Valid;
 none;
 submit data
835.739 n/a O=C(N...
GAL SIA NGA GAL C:1;
 Valid;
 none;
 submit data
819.74 n/a O=C(N...
BGC GAL SIA NGA GAL I:1;
B:1;
J:1;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
997.88 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: GAL NGA GAL SIA; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL NGA GAL SIA 1 1
2 BGC GAL SIA NGA GAL SIA 0.895238 1
3 BGC GAL GLA NGA GAL SIA 0.886792 1
4 GAL NGA GAL SIA SIA 0.87156 0.981132
5 GAL SIA NGA GAL SIA 0.826923 1
6 BGC GAL SIA NGA GAL 0.818182 1
7 BGC GAL SIA SIA 0.781818 0.981132
8 GLC GAL NGC 0.769231 0.924528
9 A2G GAL SIA 0.757282 1
10 NAG GAL SIA 0.75 1
11 SIA GAL NGA GAL 0.743119 1
12 GAL SIA NGA GAL SIA SIA 0.735043 0.981132
13 BGC GAL SIA NGA GAL FUC 0.715447 1
14 BGC GAL SIA NAG 0.710526 1
15 NAG GAL SIA SIA 0.690265 0.981132
16 NAG GAL NGC 0.6875 0.962264
17 NGA GAL SIA 0.684685 0.980769
18 GAL SIA NGA GAL 0.681416 0.981132
19 GAL NAG FUC GAL SIA 0.666667 1
20 NAG FUC GAL SIA 0.65812 1
21 NGS GAL SIA 0.655172 0.787879
22 BGC GAL SIA 0.648649 0.943396
23 NDG GAL SIA SIA 0.646552 0.945455
24 MAG FUC GAL SIA 0.644068 0.962264
25 BGC GAL SIA NGA SIA 0.632812 0.981132
26 BGC GAL NAG GAL SIA 0.629032 0.981132
27 NGA POL GAL NGC AZI 0.626016 0.784615
28 GAL SIA NGA 0.619469 1
29 BGC CEQ GAL SLB NGA GAL SIA SIA 0.615942 0.83871
30 Z3Q GAL 5N6 0.609756 0.83871
31 NAG 2FG SIA 0.594828 0.928571
32 2FG SIA 0.59434 0.892857
33 NGS FUC GLA SIA 0.59375 0.787879
34 NAG GAL PKM 0.59322 0.981132
35 GAL 5N6 0.587156 0.962264
36 GAL NAG GAL SIA 0.583333 0.981132
37 GAL SIA SIA 0.578947 0.981132
38 MBG NGC 0.568807 0.907407
39 BGC 16C GAL SIA 0.553191 0.83871
40 NAG GAL NAG GAL SIA 0.546154 0.981132
41 BGC 18C GAL SIA 0.534722 0.83871
42 BGC 18C GAL SIA NGA GAL 0.525641 0.83871
43 BGC GAL NAG GAL 0.518868 0.865385
44 BGC GAL NGA GAL 0.514286 0.865385
45 BGC GAL GLA NGA GAL 0.5 0.865385
46 NAG GAL 5N6 0.492188 0.962963
47 GAL SIA 0.468468 0.924528
48 SIA CMO 0.465347 0.87037
49 CEQ BGC NGA GAL SIA SIA 0.460526 0.8
50 BGC GAL NAG GAL FUC 0.45 0.884615
51 BGC GAL NAG 0.445455 0.865385
52 GLC GAL NAG GAL FUC GLA 0.432 0.884615
53 BGC GAL GLA NGA 0.426087 0.865385
54 NAG SIA 0.420168 0.910714
55 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.418919 0.945455
56 GLC GAL NAG GAL FUC A2G 0.415385 0.942308
57 C4W NAG FUC BMA MAN NAG GAL SIA 0.415094 0.852459
58 MAN NAG PO4 NGA PO4 0.413793 0.87931
59 MNA 0.413462 0.851852
60 SIA SIA 0.410256 0.962264
61 BGC GAL NGA 0.409091 0.865385
62 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.408284 0.852459
63 SLB SIA SIA SIA SIA 0.40678 0.962264
64 SLB SIA SIA 0.40678 0.962264
65 SIA SIA SIA SIA SIA SIA SIA 0.40678 0.962264
66 SLB SIA SIA SIA 0.40678 0.962264
67 SIA SIA SIA 0.401639 0.962264
68 BGC GAL NAG GAL FUC FUC 0.401575 0.903846
Ligand no: 2; Ligand: GAL SIA NGA GAL; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA NGA GAL 1 1
2 SIA GAL NGA GAL 0.792453 0.981132
3 BGC GAL SIA NGA GAL 0.724138 0.981132
4 GAL SIA NGA GAL SIA 0.696429 0.981132
5 GAL NGA GAL SIA 0.681416 0.981132
6 BGC GAL SIA NGA GAL SIA 0.658333 0.981132
7 A2G GAL SIA 0.645455 0.981132
8 BGC GAL GLA NGA GAL SIA 0.639344 0.981132
9 GAL SIA NGA GAL SIA SIA 0.624 0.962963
10 GAL NAG GAL SIA 0.623932 1
11 GAL SIA NGA 0.619469 0.981132
12 BGC GAL SIA NGA GAL FUC 0.610687 0.981132
13 GAL NGA GAL SIA SIA 0.606299 0.962963
14 NAG GAL SIA 0.596491 0.981132
15 NAG GAL SIA SIA 0.591667 1
16 NDG GAL SIA SIA 0.591667 0.963636
17 BGC GAL SIA NAG 0.585366 0.981132
18 NGA GAL SIA 0.584746 0.962264
19 NAG 2FG SIA 0.581197 0.912281
20 NAG FUC GAL SIA 0.577236 0.981132
21 MAG FUC GAL SIA 0.577236 0.944444
22 GAL NAG FUC GAL SIA 0.574803 0.981132
23 2FG SIA 0.564815 0.877193
24 NGS GAL SIA 0.560976 0.776119
25 NGA POL GAL NGC AZI 0.550388 0.772727
26 NAG GAL NGC 0.54918 0.944444
27 NGS FUC GLA SIA 0.545455 0.776119
28 BGC GAL SIA SIA 0.543307 0.962963
29 BGC CEQ GAL SLB NGA GAL SIA SIA 0.537931 0.825397
30 BGC GAL SIA 0.537815 0.962264
31 BGC 18C GAL SIA NGA GAL 0.535484 0.854839
32 Z3Q GAL 5N6 0.534884 0.825397
33 BGC GAL SIA NGA SIA 0.525547 0.962963
34 GLC GAL NGC 0.520661 0.907407
35 MBG NGC 0.513274 0.890909
36 GAL SIA SIA 0.512605 0.962963
37 NAG GAL NAG GAL SIA 0.511278 1
38 GAL SIA 0.509259 0.943396
39 BGC GAL NAG GAL SIA 0.507463 1
40 GAL 5N6 0.504348 0.944444
41 NAG GAL PKM 0.480315 0.962963
42 NAG GAL 5N6 0.469231 0.981481
43 SIA CMO 0.465347 0.854545
44 BGC 16C GAL SIA 0.46 0.854839
45 NAG SIA 0.456897 0.928571
46 BGC 18C GAL SIA 0.453947 0.854839
47 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.428571 0.963636
48 MNA 0.427184 0.836364
49 C4W NAG FUC BMA MAN NAG GAL SIA 0.424051 0.868852
50 A2G SER GAL 0.423423 0.890909
51 CEQ BGC NGA GAL SIA SIA 0.423077 0.815385
52 MGC GAL 0.421569 0.851852
53 GLA NAG FUC GAL 0.420168 0.886792
54 WIA SIA 0.420168 0.912281
55 BGC GAL NGA GAL 0.419643 0.849057
56 A2G THR GAL 0.419643 0.925926
57 BGC GAL NAG GAL 0.412281 0.849057
58 GAL NAG GAL FUC 0.411765 0.90566
59 SIA SIA 0.410256 0.944444
60 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.408284 0.868852
61 SLB SIA SIA 0.40678 0.944444
62 SLB SIA SIA SIA 0.40678 0.944444
63 SLB SIA SIA SIA SIA 0.40678 0.944444
64 SIA SIA SIA SIA SIA SIA SIA 0.40678 0.944444
65 A2G NPO GAL 0.405172 0.731343
66 SIA SIA SIA 0.401639 0.944444
Ligand no: 3; Ligand: BGC GAL SIA NGA GAL; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA NGA GAL 1 1
2 BGC GAL SIA NGA GAL SIA 0.917431 1
3 BGC GAL SIA NGA GAL FUC 0.841667 1
4 SIA GAL NGA GAL 0.834862 1
5 BGC GAL SIA NAG 0.830357 1
6 GAL NGA GAL SIA 0.818182 1
7 BGC GAL GLA NGA GAL SIA 0.794872 1
8 GAL SIA NGA GAL SIA 0.769912 1
9 BGC GAL SIA NGA SIA 0.738095 0.981132
10 GAL NGA GAL SIA SIA 0.725806 0.981132
11 GAL SIA NGA GAL 0.724138 0.981132
12 GAL SIA NGA GAL SIA SIA 0.690476 0.981132
13 BGC GAL SIA SIA 0.674797 0.981132
14 GAL SIA NGA 0.663793 1
15 GLC GAL NGC 0.65812 0.924528
16 BGC CEQ GAL SLB NGA GAL SIA SIA 0.652482 0.83871
17 BGC GAL SIA 0.649573 0.943396
18 BGC 18C GAL SIA NGA GAL 0.642384 0.83871
19 NAG GAL SIA 0.641026 1
20 A2G GAL SIA 0.632479 1
21 BGC GAL NAG GAL SIA 0.630769 0.981132
22 GAL NAG FUC GAL SIA 0.603053 1
23 GAL NAG GAL SIA 0.6 0.981132
24 NAG GAL NGC 0.592 0.962264
25 NAG GAL SIA SIA 0.582677 0.981132
26 NAG FUC GAL SIA 0.581395 1
27 MAG FUC GAL SIA 0.581395 0.962264
28 NGS GAL SIA 0.578125 0.787879
29 NGA GAL SIA 0.576 0.980769
30 NDG GAL SIA SIA 0.55814 0.945455
31 BGC GAL NAG GAL 0.554545 0.865385
32 NAG GAL NAG GAL SIA 0.551471 0.981132
33 BGC GAL NGA GAL 0.550459 0.865385
34 BGC GAL GLA NGA GAL 0.548673 0.865385
35 NAG 2FG SIA 0.547619 0.928571
36 NGA POL GAL NGC AZI 0.532847 0.784615
37 2FG SIA 0.529915 0.892857
38 NGS FUC GLA SIA 0.528571 0.787879
39 CEQ BGC NGA GAL SIA SIA 0.526316 0.8
40 NAG GAL PKM 0.523077 0.981132
41 Z3Q GAL 5N6 0.518248 0.83871
42 BGC 16C GAL SIA 0.506579 0.83871
43 GAL 5N6 0.5 0.962264
44 NAG GAL 5N6 0.5 0.962963
45 GAL SIA SIA 0.496063 0.981132
46 BGC 18C GAL SIA 0.490323 0.83871
47 MBG NGC 0.483607 0.907407
48 BGC GAL NAG GAL FUC 0.472 0.884615
49 GLC GAL NAG GAL FUC GLA 0.465116 0.884615
50 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.456954 0.945455
51 C4W NAG FUC BMA MAN NAG GAL SIA 0.450617 0.852459
52 BGC GAL GLA NGA 0.45 0.865385
53 BGC GAL NAG GAL FUC FUC 0.446154 0.903846
54 BGC GAL NAG 0.444444 0.865385
55 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.44186 0.852459
56 GAL SIA 0.429752 0.924528
57 GLC GAL NAG GAL FUC A2G 0.426471 0.942308
58 SIA CMO 0.423423 0.87037
59 BGC GAL NGA 0.422414 0.865385
60 BGC GAL NAG NAG GAL GAL 0.412214 0.923077
61 BGC GAL GLA 0.4 0.634615
Similar Ligands (3D)
Ligand no: 1; Ligand: GAL NGA GAL SIA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: GAL SIA NGA GAL; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 3; Ligand: BGC GAL SIA NGA GAL; Similar ligands found: 0
No: Ligand Similarity coefficient
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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