Receptor
PDB id Resolution Class Description Source Keywords
5ELB 1.08 Å NON-ENZYME: TOXIN_VIRAL CHOLERA TOXIN CLASSICAL B-PENTAMER IN COMPLEX WITH LEWIS-Y VIBRIO CHOLERAE O1 CHOLERA TOXIN B-PENTAMER LEWIS-Y COMPLEX BLOOD GROUP OLIGOSACCHARIDE/ANTIGEN TOXIN
Ref.: HIGH-RESOLUTION CRYSTAL STRUCTURES ELUCIDATE THE MO BASIS OF CHOLERA BLOOD GROUP DEPENDENCE. PLOS PATHOG. V. 12 05567 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA E:202;
D:206;
D:202;
C:201;
A:205;
E:206;
B:201;
C:204;
B:205;
A:201;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
BCN A:206;
C:206;
A:204;
B:202;
D:203;
E:201;
E:203;
C:205;
D:201;
B:206;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
163.172 C6 H13 N O4 C(CO)...
GLA H:1202;
E:205;
J:1202;
B:204;
D:205;
F:1201;
A:203;
C:203;
G:202;
I:1202;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
180.156 C6 H12 O6 C([C@...
GAL E:204;
C:202;
J:1201;
I:1201;
B:203;
A:202;
D:204;
G:203;
F:1202;
H:1201;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
180.156 C6 H12 O6 C([C@...
GAL NDG FUC FUC G:204;
I:1203;
 Valid;
Valid;
 none;
none;
 Kd = 1.1 mM
n/a n/a
PEG G:201;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
NDG GAL FUC FUC O:1;
N:1;
L:1;
Q:1;
M:1;
R:1;
K:1;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
 Kd = 1.1 mM
678.658 n/a O(C1C...
NDG FUC GAL FUC P:1;
 Valid;
 none;
 Kd = 1.1 mM
675.634 n/a O=C(N...
NAG FUC NDG GAL FUC S:1;
T:1;
 Valid;
Valid;
 none;
none;
 Kd = 1.1 mM
n/a n/a
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 NDG FUC FUC; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Ligand no: 2; Ligand: NDG GAL FUC FUC; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG GAL FUC FUC 1 1
2 BGC GAL FUC 0.605263 0.693878
3 GLC GAL BGC FUC 0.605263 0.693878
4 NAG GAL FUC FUC 0.571429 0.92
5 NAG GAL FUC A2G 0.554217 0.9
6 NDG FUC GAL FUC 0.552941 0.92
7 XYS GAL FUC 0.536585 0.68
8 MAG GAL FUC FUC 0.517241 0.901961
9 GAL FUC NGA 0.517241 0.979592
10 NAG GAL FUC 0.511628 0.9
11 MAG FUC GAL FUC 0.5 0.901961
12 BGC FUC GAL 0.5 0.693878
13 GLC BGC FUC GAL 0.5 0.693878
14 GAL NAG GAL FUC FUC 0.5 0.92
15 GLA NAG GAL FUC 0.473118 0.9
16 BHE 0.465116 0.614035
17 BGC GAL FUC GLA 0.460674 0.693878
18 4YA 0.458824 0.614035
19 GAL NAG GAL FUC 0.458333 0.865385
20 BGC GAL NAG GAL FUC FUC 0.456311 0.92
21 NAG FUC GAL 0.454545 0.9
22 BGC GAL NAG GAL FUC 0.445545 0.9
23 GAL FUC GAL 0.433735 0.693878
24 NAG GAL FUC GLA 0.42268 0.9
25 NAG NON FUC GAL FUC 0.419048 0.793103
26 NAG GAL FUC FUC A2G 0.407767 0.884615
27 MAN MAN MAN GLC 0.406977 0.673469
28 BGC FUC GAL FUC A2G 0.405941 0.92
29 BGC GAL FUC A2G 0.401961 0.9
Ligand no: 3; Ligand: NDG FUC GAL FUC; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG FUC GAL FUC 1 1
2 NAG GAL FUC FUC 0.940298 1
3 NAG FUC GAL 0.8 0.978723
4 MAG FUC GAL FUC 0.756757 0.979167
5 NAG GAL FUC 0.753425 0.978723
6 NAG GAL FUC A2G 0.739726 0.978723
7 MAG GAL FUC FUC 0.710526 0.979167
8 NAG FUC GAL FUC A2G 0.702381 0.959184
9 NAG GAL FUC FUC A2G 0.662791 0.959184
10 GAL NAG GAL FUC FUC 0.654762 1
11 MAG SGA FUC 0.642857 0.71875
12 GLA NAG GAL FUC 0.607143 0.978723
13 NAG FUC 0.60274 0.957447
14 BGC GAL FUC 0.6 0.723404
15 GLC GAL BGC FUC 0.6 0.723404
16 NAG NON FUC GAL FUC 0.597826 0.854545
17 BGC GAL NAG GAL FUC FUC 0.591398 1
18 GAL NAG GAL FUC 0.568182 0.938776
19 BGC GAL NAG GAL FUC 0.565217 0.978723
20 NAG GAL FUC GLA 0.563218 0.978723
21 NDG GAL FUC FUC 0.552941 0.92
22 GAL NAG FUC GAL 0.551724 0.978723
23 XYS GAL FUC 0.55 0.708333
24 BGC FUC GAL FUC A2G 0.538462 1
25 BGC FUC GAL 0.512821 0.723404
26 GLC BGC FUC GAL 0.512821 0.723404
27 GLA NAG FUC GAL 0.51087 0.958333
28 GAL FUC A2G 0.505882 0.978723
29 MAG FUC G4S 0.505495 0.707692
30 BGC GAL FUC A2G 0.5 0.978723
31 BGC FUC GAL NAG 0.494624 0.978723
32 NAG GAL 0.493506 0.957447
33 A2G GAL 0.493506 0.957447
34 NAG FUC GAL SIA 0.490909 0.903846
35 MAG FUC SGA 0.483871 0.707692
36 BGC FUC GAL NAG GAL 0.479592 0.978723
37 BHE 0.47619 0.636364
38 AMU NAG 0.47191 0.94
39 4YA 0.46988 0.636364
40 GLC GAL NAG GAL FUC GLA 0.460784 0.978723
41 A2G NAG 0.45679 0.938776
42 BGC GAL FUC GLA 0.454545 0.723404
43 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.45098 0.957447
44 NAG NAG BMA MAN NAG 0.44898 0.959184
45 NDG NAG GLA NAG GLC RAM 0.448598 0.959184
46 NDG GLA NAG GLC RAM 0.448598 0.959184
47 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.446602 0.957447
48 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.445545 0.94
49 GAL FUC GAL 0.444444 0.723404
50 NAG GAL GAL 0.44186 0.957447
51 GLC GAL NAG GAL FUC A2G 0.439252 0.959184
52 GDL NAG 0.439024 0.938776
53 NDG GLA GLC NAG GLC RAM 0.436364 0.959184
54 MAN MAN NAG 0.433333 0.918367
55 MAN NAG GAL 0.431818 0.957447
56 NAG GAL BGC GAL 0.428571 0.957447
57 MMA MAN NAG 0.426966 0.958333
58 NAG G6S 0.426966 0.703125
59 NAG TA5 FUC 0.425532 0.69697
60 NAG BMA MAN MAN NAG GAL NAG GAL 0.424528 0.959184
61 TVD GAL 0.419753 0.92
62 NAG NAG NAG NAG NAG NAG 0.418605 0.959184
63 NDG NAG NAG NAG NAG 0.418605 0.959184
64 NAG NAG NAG NAG NAG 0.418605 0.959184
65 NAG NAG NAG NAG NAG NAG NAG NAG 0.418605 0.959184
66 ASG GC4 0.414894 0.676923
67 MAN NAG 0.414634 0.957447
68 HSH A2G FUC 0.414141 0.854545
69 BGC GAL SIA NGA GAL FUC 0.414062 0.903846
70 MAN MAN MAN NAG NAG 0.412371 0.938776
71 A2G GAL NAG 0.408602 0.938776
72 ASG IDR ASG IDR 0.407767 0.707692
73 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.40708 0.938776
74 NAG BDP 0.406977 0.918367
75 NDG BMA MAN MAN NAG GAL NAG 0.405405 0.959184
76 BGC GAL NGA 0.404494 0.957447
77 NAG GAL NAG GAL NAG GAL 0.404255 0.959184
78 NAG GAL NAG GAL 0.404255 0.938776
79 NGS FUC GLA SIA 0.403226 0.712121
80 MGC GAL 0.402439 0.958333
81 BGC GAL NGA GAL 0.402174 0.957447
82 NAG GAL NAG 0.402174 0.938776
83 BMA MAN MAN NAG GAL NAG 0.401869 0.938776
84 NAG NAG BMA MAN MAN NAG GAL NAG 0.401786 0.959184
85 NDG BMA MAN MAN NAG MAN MAN 0.401786 0.938776
86 MAN MAN MAN GLC 0.4 0.702128
87 NAG BDP NAG BDP NAG BDP NAG 0.4 0.94
Ligand no: 4; Ligand: NAG FUC NDG GAL FUC; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: GAL NDG FUC FUC; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: NDG GAL FUC FUC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 NAG FUC GAL FUC 0.9593
Ligand no: 3; Ligand: NDG FUC GAL FUC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 NAG FUC GAL FUC 0.9659
Ligand no: 4; Ligand: NAG FUC NDG GAL FUC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 NAG FUC NDG GAL FUC 1.0000
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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