Receptor
PDB id Resolution Class Description Source Keywords
3BVX 1.1 Å EC: 3.2.1.114 GOLGI MANNOSIDASE II D204A CATALYTIC NUCLEOPHILE MUTANT COMPLEX WITH METHYL (2-DEOXY-2-ACETAMIDO-BETA-D- G LUCOPYRANOSYL)-(1->2)-(ALPHA-D-MANNOPYRANOSYL)- (1->3)- [( ALPHA-D-MANNOPYRANOSYL)-(1->6)-(ALPHA-D-MANNOPYRANOSYL)- (1- >6)]-BETA-D DROSOPHILA MELANOGASTER FAMILY 38 GLYCOYSL HYDROLASE GLYCOSIDASE GOLGI APPARATUS MEMBRANE SIGNAL-ANCHOR TRANSMEMBRANE
Ref.: PROBING THE SUBSTRATE SPECIFICITY OF GOLGI ALPHA-MANNOSIDASE II BY USE OF SYNTHETIC OLIGOSACCHARIDES AND A CATALYTIC NUCLEOPHILE MUTANT. J.AM.CHEM.SOC. V. 130 8975 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MPD A:1048;
Invalid;
none;
submit data
118.174 C6 H14 O2 C[C@@...
WZ5 A:1047;
Valid;
none;
submit data
883.797 C33 H57 N O26 CC(=O...
ZN A:1046;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EJR 1.27 Å EC: 3.2.1.114 GOLGI ALPHA-MANNOSIDASE II IN COMPLEX WITH 5-SUBSTITUED SWAI ANALOG: (5R)-5-[2'-OXO-2'-(4-TERT-BUTYLPHENYL)ETHYL]-SWAINS DROSOPHILA MELANOGASTER GH38 GLYCOSIDASE GLYCOSIDASE GOLGI APPARATUS HYDROLASE MMETAL-BINDING SIGNAL-ANCHOR TRANSMEMBRANE
Ref.: STRUCTURAL INVESTIGATION OF THE BINDING OF 5-SUBSTI SWAINSONINE ANALOGUES TO GOLGI ALPHA-MANNOSIDASE II CHEMBIOCHEM V. 11 673 2010
Members (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OW7 ic50 = 14 uM NK2 C8 H15 O2 S C1CC[S@@+]....
2 3D51 Ki = 70 uM GOX C6 H12 N2 O5 C([C@@H]1[....
3 3CV5 - M5S C30 H52 O26 C([C@@H]1[....
4 3EJS ic50 = 250 nM HN5 C20 H31 N O3 CC(C)(C)c1....
5 3DX0 Ki = 36 nM MSN C6 H13 N O3 S CS[C@@H]1[....
6 2FYV ic50 = 0.3 mM W72 C11 H21 N O9 C1[C@H]([C....
7 3BVW - WZ4 C33 H57 N O25 S CC(=O)N[C@....
8 3D4Z Ki = 13 uM GIM C8 H13 N2 O4 c1c[n+]2c(....
9 1TQU ic50 ~ 7.5 mM GHA C9 H18 N O9 S C1C([C@@H]....
10 3DDG Ki = 1 uM GB7 C14 H20 N2 O4 CN1[C@@H](....
11 1PS3 Ki = 5.2 mM KIF C8 H12 N2 O6 C([C@@H]1[....
12 3DX2 Ki = 150 nM MZB C6 H13 N O4 S C[S@@](=O)....
13 2F7O Ki = 0.036 uM MSN C6 H13 N O3 S CS[C@@H]1[....
14 3D52 Ki = 520 uM GHR C13 H16 Cl N3 O6 c1cc(ccc1N....
15 1TQV ic50 ~ 7.5 mM SSE C9 H18 O9 S Se C1[C@H]([C....
16 3EJU ic50 = 250 nM HN7 C20 H29 N O4 CC(C)(C)c1....
17 1HXK ic50 = 400 uM DMJ C6 H13 N O4 C1[C@H]([C....
18 1TQS - SSO C9 H18 O9 S2 C1[C@H]([C....
19 3CZN - M5G C46 H78 N2 O36 CC(=O)N[C@....
20 2OW6 ic50 = 2 mM NK1 C8 H15 O3 S C1C[C@@H](....
21 3BUP - MAN C6 H12 O6 C([C@@H]1[....
22 3EJT ic50 = 44 nM HN6 C20 H31 N O3 CC(C)(C)c1....
23 3CZS - MAN C6 H12 O6 C([C@@H]1[....
24 3DX1 Ki = 265 uM YHO C5 H11 N O3 C1[C@H]([C....
25 2F7P Ki = 0.249 uM 2SK C13 H19 N O3 S CS[C@@H]1[....
26 3EJP Ki = 2.8 nM HN2 C16 H21 N O4 c1ccc(cc1)....
27 3BVV - WZ3 C19 H34 O15 S CO[C@H]1[C....
28 2F18 ic50 = 80 uM GB1 C13 H20 N2 O3 c1ccc(cc1)....
29 3DX4 Ki = 76 nM GOO C6 H13 N O4 CO[C@@H]1[....
30 2F1A ic50 = 720 uM GB2 C13 H20 N2 O3 c1ccc(cc1)....
31 3D4Y Ki = 2 uM MVL C8 H12 N2 O4 c1cn2c(n1)....
32 3DDF Ki = 67 uM GB6 C13 H18 N2 O4 c1ccc(cc1)....
33 1TQT ic50 ~ 7.5 mM SSD C9 H18 O9 S2 C1[C@H]([C....
34 3DX3 Ki = 300 nM YTB C5 H11 N O4 C1([C@H]([....
35 3BUQ - MAN C6 H12 O6 C([C@@H]1[....
36 3EJR Ki = 2.7 nM HN4 C20 H29 N O4 CC(C)(C)c1....
37 1R34 ic50 = 0.9 mM LKS C14 H20 N2 O4 S [H]/N=C(/C....
38 3BVX - WZ5 C33 H57 N O26 CC(=O)N[C@....
39 1HWW ic50 = 20 nM SWA C8 H15 N O3 C1C[C@H]([....
40 3EJQ Ki = 2.7 nM HN3 C17 H23 N O4 Cc1ccc(cc1....
41 3D50 Ki = 17 uM OEV C15 H29 N O4 CCCCCCCCN[....
42 2F1B ic50 = 1000 uM GB3 C14 H22 N2 O3 C[C@@H]1[C....
43 1R33 ic50 = 0.07 mM LKA C6 H13 N O4 S C([C@@H]1[....
44 1TQW ic50 ~ 7.5 mM BLT C9 H18 O9 S Se C1[C@H]([C....
45 3BVT - WZ1 C13 H24 O10 S CO[C@@H]1[....
46 3BVU - WZ2 C19 H34 O15 S CO[C@@H]1[....
70% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OW7 ic50 = 14 uM NK2 C8 H15 O2 S C1CC[S@@+]....
2 3D51 Ki = 70 uM GOX C6 H12 N2 O5 C([C@@H]1[....
3 3CV5 - M5S C30 H52 O26 C([C@@H]1[....
4 3EJS ic50 = 250 nM HN5 C20 H31 N O3 CC(C)(C)c1....
5 3DX0 Ki = 36 nM MSN C6 H13 N O3 S CS[C@@H]1[....
6 2FYV ic50 = 0.3 mM W72 C11 H21 N O9 C1[C@H]([C....
7 3BVW - WZ4 C33 H57 N O25 S CC(=O)N[C@....
8 3D4Z Ki = 13 uM GIM C8 H13 N2 O4 c1c[n+]2c(....
9 1TQU ic50 ~ 7.5 mM GHA C9 H18 N O9 S C1C([C@@H]....
10 3DDG Ki = 1 uM GB7 C14 H20 N2 O4 CN1[C@@H](....
11 1PS3 Ki = 5.2 mM KIF C8 H12 N2 O6 C([C@@H]1[....
12 3DX2 Ki = 150 nM MZB C6 H13 N O4 S C[S@@](=O)....
13 2F7O Ki = 0.036 uM MSN C6 H13 N O3 S CS[C@@H]1[....
14 3D52 Ki = 520 uM GHR C13 H16 Cl N3 O6 c1cc(ccc1N....
15 1TQV ic50 ~ 7.5 mM SSE C9 H18 O9 S Se C1[C@H]([C....
16 3EJU ic50 = 250 nM HN7 C20 H29 N O4 CC(C)(C)c1....
17 1HXK ic50 = 400 uM DMJ C6 H13 N O4 C1[C@H]([C....
18 1TQS - SSO C9 H18 O9 S2 C1[C@H]([C....
19 3CZN - M5G C46 H78 N2 O36 CC(=O)N[C@....
20 2OW6 ic50 = 2 mM NK1 C8 H15 O3 S C1C[C@@H](....
21 3BUP - MAN C6 H12 O6 C([C@@H]1[....
22 3EJT ic50 = 44 nM HN6 C20 H31 N O3 CC(C)(C)c1....
23 3CZS - MAN C6 H12 O6 C([C@@H]1[....
24 3DX1 Ki = 265 uM YHO C5 H11 N O3 C1[C@H]([C....
25 2F7P Ki = 0.249 uM 2SK C13 H19 N O3 S CS[C@@H]1[....
26 3EJP Ki = 2.8 nM HN2 C16 H21 N O4 c1ccc(cc1)....
27 3BVV - WZ3 C19 H34 O15 S CO[C@H]1[C....
28 2F18 ic50 = 80 uM GB1 C13 H20 N2 O3 c1ccc(cc1)....
29 3DX4 Ki = 76 nM GOO C6 H13 N O4 CO[C@@H]1[....
30 2F1A ic50 = 720 uM GB2 C13 H20 N2 O3 c1ccc(cc1)....
31 3D4Y Ki = 2 uM MVL C8 H12 N2 O4 c1cn2c(n1)....
32 3DDF Ki = 67 uM GB6 C13 H18 N2 O4 c1ccc(cc1)....
33 1TQT ic50 ~ 7.5 mM SSD C9 H18 O9 S2 C1[C@H]([C....
34 3DX3 Ki = 300 nM YTB C5 H11 N O4 C1([C@H]([....
35 3BUQ - MAN C6 H12 O6 C([C@@H]1[....
36 3EJR Ki = 2.7 nM HN4 C20 H29 N O4 CC(C)(C)c1....
37 1R34 ic50 = 0.9 mM LKS C14 H20 N2 O4 S [H]/N=C(/C....
38 3BVX - WZ5 C33 H57 N O26 CC(=O)N[C@....
39 1HWW ic50 = 20 nM SWA C8 H15 N O3 C1C[C@H]([....
40 3EJQ Ki = 2.7 nM HN3 C17 H23 N O4 Cc1ccc(cc1....
41 3D50 Ki = 17 uM OEV C15 H29 N O4 CCCCCCCCN[....
42 2F1B ic50 = 1000 uM GB3 C14 H22 N2 O3 C[C@@H]1[C....
43 1R33 ic50 = 0.07 mM LKA C6 H13 N O4 S C([C@@H]1[....
44 1TQW ic50 ~ 7.5 mM BLT C9 H18 O9 S Se C1[C@H]([C....
45 3BVT - WZ1 C13 H24 O10 S CO[C@@H]1[....
46 3BVU - WZ2 C19 H34 O15 S CO[C@@H]1[....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OW7 ic50 = 14 uM NK2 C8 H15 O2 S C1CC[S@@+]....
2 3D51 Ki = 70 uM GOX C6 H12 N2 O5 C([C@@H]1[....
3 3CV5 - M5S C30 H52 O26 C([C@@H]1[....
4 3EJS ic50 = 250 nM HN5 C20 H31 N O3 CC(C)(C)c1....
5 3DX0 Ki = 36 nM MSN C6 H13 N O3 S CS[C@@H]1[....
6 2FYV ic50 = 0.3 mM W72 C11 H21 N O9 C1[C@H]([C....
7 3BVW - WZ4 C33 H57 N O25 S CC(=O)N[C@....
8 3D4Z Ki = 13 uM GIM C8 H13 N2 O4 c1c[n+]2c(....
9 1TQU ic50 ~ 7.5 mM GHA C9 H18 N O9 S C1C([C@@H]....
10 3DDG Ki = 1 uM GB7 C14 H20 N2 O4 CN1[C@@H](....
11 1PS3 Ki = 5.2 mM KIF C8 H12 N2 O6 C([C@@H]1[....
12 3DX2 Ki = 150 nM MZB C6 H13 N O4 S C[S@@](=O)....
13 2F7O Ki = 0.036 uM MSN C6 H13 N O3 S CS[C@@H]1[....
14 3D52 Ki = 520 uM GHR C13 H16 Cl N3 O6 c1cc(ccc1N....
15 1TQV ic50 ~ 7.5 mM SSE C9 H18 O9 S Se C1[C@H]([C....
16 3EJU ic50 = 250 nM HN7 C20 H29 N O4 CC(C)(C)c1....
17 1HXK ic50 = 400 uM DMJ C6 H13 N O4 C1[C@H]([C....
18 1TQS - SSO C9 H18 O9 S2 C1[C@H]([C....
19 3CZN - M5G C46 H78 N2 O36 CC(=O)N[C@....
20 2OW6 ic50 = 2 mM NK1 C8 H15 O3 S C1C[C@@H](....
21 3BUP - MAN C6 H12 O6 C([C@@H]1[....
22 3EJT ic50 = 44 nM HN6 C20 H31 N O3 CC(C)(C)c1....
23 3CZS - MAN C6 H12 O6 C([C@@H]1[....
24 3DX1 Ki = 265 uM YHO C5 H11 N O3 C1[C@H]([C....
25 2F7P Ki = 0.249 uM 2SK C13 H19 N O3 S CS[C@@H]1[....
26 3EJP Ki = 2.8 nM HN2 C16 H21 N O4 c1ccc(cc1)....
27 3BVV - WZ3 C19 H34 O15 S CO[C@H]1[C....
28 2F18 ic50 = 80 uM GB1 C13 H20 N2 O3 c1ccc(cc1)....
29 3DX4 Ki = 76 nM GOO C6 H13 N O4 CO[C@@H]1[....
30 2F1A ic50 = 720 uM GB2 C13 H20 N2 O3 c1ccc(cc1)....
31 3D4Y Ki = 2 uM MVL C8 H12 N2 O4 c1cn2c(n1)....
32 3DDF Ki = 67 uM GB6 C13 H18 N2 O4 c1ccc(cc1)....
33 1TQT ic50 ~ 7.5 mM SSD C9 H18 O9 S2 C1[C@H]([C....
34 3DX3 Ki = 300 nM YTB C5 H11 N O4 C1([C@H]([....
35 3BUQ - MAN C6 H12 O6 C([C@@H]1[....
36 3EJR Ki = 2.7 nM HN4 C20 H29 N O4 CC(C)(C)c1....
37 1R34 ic50 = 0.9 mM LKS C14 H20 N2 O4 S [H]/N=C(/C....
38 3BVX - WZ5 C33 H57 N O26 CC(=O)N[C@....
39 1HWW ic50 = 20 nM SWA C8 H15 N O3 C1C[C@H]([....
40 3EJQ Ki = 2.7 nM HN3 C17 H23 N O4 Cc1ccc(cc1....
41 3D50 Ki = 17 uM OEV C15 H29 N O4 CCCCCCCCN[....
42 2F1B ic50 = 1000 uM GB3 C14 H22 N2 O3 C[C@@H]1[C....
43 1R33 ic50 = 0.07 mM LKA C6 H13 N O4 S C([C@@H]1[....
44 1TQW ic50 ~ 7.5 mM BLT C9 H18 O9 S Se C1[C@H]([C....
45 3BVT - WZ1 C13 H24 O10 S CO[C@@H]1[....
46 3BVU - WZ2 C19 H34 O15 S CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: WZ5; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 WZ5 1 1
2 WZ4 0.773196 0.94
3 NAG MAN MMA 0.719512 1
4 M5G 0.693069 0.938776
5 NAG MAN MAN MAN NAG 0.623656 0.938776
6 NAG BMA MAN MAN MAN MAN MAN 0.615385 0.734694
7 MMA MAN NAG MAN NAG NAG 0.610526 0.94
8 NAG MAN BMA NDG MAN NAG GAL 0.603774 0.92
9 NAG MBG 0.590361 1
10 MAN MMA MAN 0.590361 0.744681
11 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.588235 0.957447
12 NAG MAN MAN 0.582418 0.957447
13 NAG MAN BMA 0.582418 0.957447
14 NAG BMA NAG MAN MAN NAG NAG 0.580952 0.92
15 3PV 0.571429 0.94
16 NAG NAG BMA MAN MAN MAN MAN 0.5625 0.867925
17 NAG MAN MAN MAN NAG GAL NAG GAL 0.556604 0.92
18 NAG MAN GAL BMA NDG MAN NAG GAL 0.556604 0.92
19 MAN BMA NAG NAG MAN NAG GAL GAL 0.556604 0.92
20 NAG MAN GAL BMA NAG MAN NAG GAL 0.556604 0.92
21 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.544643 0.938776
22 NAG NAG BMA MAN MAN NAG NAG 0.544643 0.851852
23 NAG MAN GAL MAN MAN NAG GAL 0.543689 0.938776
24 1GN ACY GAL ACY 1GN BGC GAL BGC 0.529412 0.938776
25 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.529412 0.938776
26 NAG NAG BMA MAN MAN 0.528846 0.938776
27 MAN MAN NAG MAN NAG 0.528846 0.938776
28 WZ3 0.527473 0.729167
29 MAN MAN NAG 0.521277 0.918367
30 NAG BMA MAN MAN MAN MAN 0.514852 0.957447
31 MBG A2G 0.511364 1
32 A2G MBG 0.511364 1
33 MAN MAN MAN BMA MAN MAN MAN 0.504951 0.744681
34 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.504505 0.882353
35 ASN NAG NAG BMA MAN MAN NAG NAG 0.504132 0.836364
36 NAG NAG BMA MAN NAG 0.495495 0.851852
37 MAN MMA 0.493827 0.744681
38 MAN MAN BMA MAN 0.483516 0.702128
39 MAN MAN MAN MAN 0.483516 0.702128
40 MAN MAN MAN BMA MAN 0.463918 0.702128
41 MAN NAG 0.460674 0.957447
42 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.457944 0.641509
43 NGA GAL 0.455556 0.957447
44 GAL NAG 0.455556 0.957447
45 NAG GAL 0.455556 0.957447
46 NAG NGA 0.450549 0.938776
47 NAG A2G 0.450549 0.938776
48 M5S 0.446809 0.702128
49 MAN BMA MAN MAN MAN 0.446809 0.702128
50 KDO MAN MAN MAN MAN MAN 0.445378 0.666667
51 NAG GAL BGC 0.444444 0.957447
52 NAG NM9 0.444444 0.921569
53 NAG GAL NAG 0.444444 0.938776
54 NDG NAG 0.44086 0.92
55 MAN H1M MAN 0.4375 0.7
56 NGA GLA GAL BGC 0.436893 0.957447
57 NAG GDL 0.434783 0.938776
58 NAG NDG 0.434783 0.938776
59 GLC GLC GLC GLC 0.434783 0.702128
60 CBS 0.434783 0.938776
61 CBS CBS 0.434783 0.938776
62 MAG 0.433735 0.93617
63 2F8 0.433735 0.93617
64 AXR BXY BXY BXX 0.428571 0.673469
65 OPM MAN MAN 0.428571 0.62963
66 NAG GAL 2NA 0.426087 0.849057
67 GAL BGC NAG GAL 0.425743 0.957447
68 NGA GAL FUC 0.42 0.978723
69 A2G GAL FUC 0.42 0.978723
70 FUC GLA A2G 0.42 0.978723
71 A2G GLA FUC 0.42 0.978723
72 FUC GL0 A2G 0.42 0.978723
73 FUC GAL A2G 0.42 0.978723
74 GLC GLC GLC GLC BGC 0.418605 0.702128
75 GLC GLC GLC 0.418605 0.702128
76 MAN MAN MAN 0.418605 0.702128
77 GLC GLC GLC GLC GLC BGC 0.418605 0.702128
78 NGA GAL BGC 0.418367 0.957447
79 CTO 0.416667 0.92
80 NDG NAG NAG 0.416667 0.92
81 NDG NAG NAG NDG 0.416667 0.92
82 NDG NAG NAG NDG NAG 0.416667 0.92
83 NAG NAG NAG NAG NAG NAG 0.416667 0.92
84 NAG NAG NAG NAG NDG NAG 0.416667 0.92
85 NAG NAG NAG NAG NDG 0.416667 0.92
86 NAG NAG NDG 0.416667 0.92
87 FUC BGC GAL NAG 0.416667 0.978723
88 NAG AMU NAG AMV 0.416667 0.921569
89 NAG NAG NAG NAG 0.416667 0.92
90 NAG NAG NAG NAG NAG NAG NAG NAG 0.416667 0.92
91 NAG NAG NAG NAG NAG 0.416667 0.92
92 NAG NAG NAG NDG 0.416667 0.92
93 NAG NAG NAG 0.416667 0.92
94 NDG NAG NAG NAG 0.416667 0.92
95 LEC NGA 0.415094 0.707692
96 NAG NGO 0.414141 0.867925
97 GLC GAL NAG GAL 0.413462 0.957447
98 WZ2 0.412371 0.7
99 FUC GAL MAG FUC 0.411765 0.979167
100 A2G GAL NAG FUC 0.409091 0.92
101 A2G GAL BGC FUC 0.409091 0.978723
102 MDM 0.406977 0.744681
103 GAL MBG 0.406977 0.744681
104 M13 0.406977 0.744681
105 3QL 0.40404 0.867925
106 NAG GAL GAL NAG GAL 0.403846 0.938776
107 GAL NAG GAL NAG GAL NAG 0.403846 0.92
108 NAG GAL GAL NAG 0.403846 0.938776
109 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.403509 0.94
110 GAL MGC 0.402174 1
111 NAG NAG 0.402062 0.849057
112 6Y2 0.401869 0.707692
113 FUC GAL NAG A2G FUC 0.401786 0.92
114 NAG GAL FUC FUC A2G 0.401786 0.92
115 MAN NAG GAL 0.4 0.957447
116 GLC FUC GAL FUC A2G 0.4 0.958333
117 A2G GAL NAG FUC GAL GLC 0.4 0.92
118 GLC GAL NAG GAL FUC A2G 0.4 0.92
119 GAL NAG MAN 0.4 0.957447
120 BGC FUC GAL FUC A2G 0.4 0.958333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EJR; Ligand: HN4; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 3ejr.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BQF SSM 0.03675 0.40207 2.57732
2 3AJ6 NGA 0.0427 0.40179 2.7972
3 4OWK NGA 0.01797 0.42672 2.89855
4 4CQB MLI 0.02979 0.4143 5.67376
5 5H9O OXM 0.0001484 0.51186 6.30105
6 5D4Y BXP 0.0342 0.41092 14.6479
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