Receptor
PDB id Resolution Class Description Source Keywords
3BUP 2.03 Å EC: 3.2.1.114 GOLGI ALPHA-MANNOSIDASE II D341N ACID-BASE CATALYST MUTANT W MANNOSE DROSOPHILA MELANOGASTER GLYCOSYL HYDROLASE FAMILY 38 GLYCOSIDASE GOLGI APPARATUS SIGNAL-ANCHOR TRANSMEMBRANE HYDROLASE
Ref.: PROBING THE SUBSTRATE SPECIFICITY OF GOLGI ALPHA-MA II BY USE OF SYNTHETIC OLIGOSACCHARIDES AND A CATAL 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
MAN A:1047;
Valid;
none;
submit data
180.156 C6 H12 O6 C([C@...
MPD A:1049;
Invalid;
none;
submit data
118.174 C6 H14 O2 C[C@@...
NAG A:1046;
Invalid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
ZN A:1048;
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: MAN; Similar ligands found: 142
No: Ligand ECFP6 Tc MDL keys Tc
1 WOO 1 1
2 GLC 1 1
3 BGC 1 1
4 ALL 1 1
5 BMA 1 1
6 GXL 1 1
7 GIV 1 1
8 GAL 1 1
9 MAN 1 1
10 GLA 1 1
11 Z6J 0.653846 0.866667
12 32O 0.653846 0.866667
13 RIB 0.653846 0.866667
14 FUB 0.653846 0.866667
15 AHR 0.653846 0.866667
16 MLB 0.511628 0.848485
17 GLC GLC 0.511628 0.848485
18 BGC GLC 0.511628 0.848485
19 BGC GLA 0.511628 0.848485
20 GLA BMA 0.511628 0.848485
21 MAN BMA 0.511628 0.848485
22 BMA GLA 0.511628 0.848485
23 GLA BGC 0.511628 0.848485
24 MAN MAN 0.511628 0.848485
25 GLA GLC 0.511628 0.848485
26 BMA MAN 0.511628 0.848485
27 GAL GLC 0.511628 0.848485
28 GAL GAL 0.511628 0.848485
29 LAK 0.511628 0.848485
30 GLC BGC 0.511628 0.848485
31 YDR 0.5 0.8
32 GLC GLC GLC GLC BGC 0.488889 0.848485
33 GLC GLC GLC 0.488889 0.848485
34 MAN MAN MAN 0.488889 0.848485
35 BMA MAN MAN 0.488889 0.848485
36 GLC GLC GLC GLC GLC BGC 0.488889 0.848485
37 EMZ 0.472222 0.794118
38 BG6 0.461538 0.675
39 BGP 0.461538 0.675
40 G6P 0.461538 0.675
41 M6P 0.461538 0.675
42 M6D 0.461538 0.675
43 A6P 0.461538 0.675
44 GAF 0.457143 0.875
45 SHG 0.457143 0.875
46 2FG 0.457143 0.875
47 G2F 0.457143 0.875
48 2H5 0.457143 0.875
49 GCS 0.457143 0.777778
50 1GN 0.457143 0.777778
51 X6X 0.457143 0.777778
52 PA1 0.457143 0.777778
53 95Z 0.457143 0.777778
54 G3F 0.457143 0.875
55 NGR 0.454545 0.848485
56 MAL 0.454545 0.848485
57 MAN GLC 0.454545 0.848485
58 GAL BGC 0.454545 0.848485
59 GLA GLA 0.454545 0.848485
60 BGC BMA 0.454545 0.848485
61 M3M 0.454545 0.848485
62 GLA GAL 0.454545 0.848485
63 MAB 0.454545 0.848485
64 GLC GAL 0.454545 0.848485
65 B2G 0.454545 0.848485
66 LBT 0.454545 0.848485
67 BMA GAL 0.454545 0.848485
68 LAT 0.454545 0.848485
69 BGC GAL 0.454545 0.848485
70 CBI 0.454545 0.848485
71 CBK 0.454545 0.848485
72 N9S 0.454545 0.848485
73 LB2 0.454545 0.848485
74 3MG 0.444444 0.875
75 TCB 0.444444 0.8
76 GLC SGC 0.444444 0.8
77 YIO 0.441176 0.870968
78 2GS 0.432432 0.875
79 2M4 0.431818 0.848485
80 AHR AHR 0.428571 0.764706
81 GLF 0.428571 0.84375
82 FUB AHR 0.428571 0.764706
83 MAN BMA BMA 0.416667 0.848485
84 BMA MAN BMA 0.416667 0.848485
85 CTR 0.416667 0.848485
86 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.848485
87 GLA GAL BGC 0.416667 0.848485
88 CE5 0.416667 0.848485
89 MLR 0.416667 0.848485
90 CE6 0.416667 0.848485
91 MT7 0.416667 0.848485
92 BMA BMA BMA 0.416667 0.848485
93 GLC BGC BGC BGC BGC 0.416667 0.848485
94 MAN MAN BMA BMA BMA BMA 0.416667 0.848485
95 BGC BGC BGC BGC BGC 0.416667 0.848485
96 BGC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
97 BGC GLC GLC 0.416667 0.848485
98 BMA BMA BMA BMA BMA 0.416667 0.848485
99 MAN BMA BMA BMA BMA 0.416667 0.848485
100 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
101 GLC BGC BGC BGC BGC BGC 0.416667 0.848485
102 MAN BMA BMA BMA BMA BMA 0.416667 0.848485
103 BGC BGC BGC BGC BGC BGC 0.416667 0.848485
104 BGC GLC GLC GLC 0.416667 0.848485
105 BGC BGC BGC GLC 0.416667 0.848485
106 CTT 0.416667 0.848485
107 GLA GAL GLC 0.416667 0.848485
108 MTT 0.416667 0.848485
109 GLC BGC BGC BGC 0.416667 0.848485
110 GLC GLC BGC 0.416667 0.848485
111 CEY 0.416667 0.848485
112 B4G 0.416667 0.848485
113 CE8 0.416667 0.848485
114 BMA BMA BMA BMA BMA BMA 0.416667 0.848485
115 GAL FUC 0.416667 0.848485
116 DXI 0.416667 0.848485
117 GLC BGC GLC 0.416667 0.848485
118 CT3 0.416667 0.848485
119 GAL GAL GAL 0.416667 0.848485
120 GLC GLC GLC GLC GLC 0.416667 0.848485
121 BGC BGC BGC BGC 0.416667 0.848485
122 BGC BGC BGC 0.416667 0.848485
123 BGC BGC GLC 0.416667 0.848485
124 CEX 0.416667 0.848485
125 GLC GAL GAL 0.416667 0.848485
126 BGC GLC GLC GLC GLC 0.416667 0.848485
127 GLC BGC BGC 0.416667 0.848485
128 GS1 GLC GS1 0.408163 0.8
129 SGC SGC BGC 0.408163 0.8
130 BGC BGC BGC GLC BGC BGC 0.408163 0.848485
131 GLC BGC BGC BGC BGC BGC BGC 0.408163 0.848485
132 1LL 0.405405 0.771429
133 TDG 0.405405 0.771429
134 TRE 0.405405 0.848485
135 NDG 0.404762 0.7
136 NGA 0.404762 0.7
137 NAG 0.404762 0.7
138 HSQ 0.404762 0.7
139 A2G 0.404762 0.7
140 BM3 0.404762 0.7
141 FUB AHR AHR 0.4 0.764706
142 AHR AHR AHR AHR AHR AHR 0.4 0.764706
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3EJR; Ligand: HN4; 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: 3ejr.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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