Receptor
PDB id Resolution Class Description Source Keywords
3CZN 1.4 Å EC: 3.2.1.114 GOLGI ALPHA-MANNOSIDASE II (D204A NUCLEOPHILE MUTANT) IN COM GNMAN5GN DROSOPHILA MELANOGASTER HYDROLASE GLYCOSYL HYDROLASE MANNOSIDASE N-TERMINAL ALPHADOMAIN THREE HELIX BUNDLE 2 C-TERMINAL BETA BARRELS GLYCGOLGI APPARATUS MEMBRANE METAL-BINDING SIGNAL-ANCHOR TRANSMEMBRANE
Ref.: GOLGI ALPHA-MANNOSIDASE II CLEAVES TWO SUGARS SEQUE IN THE SAME CATALYTIC SITE. PROC.NATL.ACAD.SCI.USA V. 105 9570 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:1101;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
ZN A:1102;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
NDG BMA MAN MAN NAG MAN MAN B:1;
 Valid;
 none;
 submit data
1235.11 n/a O=C(N...
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 - BMA MAN MAN MAN MAN n/a n/a
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 - YZ0 MAN Z4Y NAG MAN n/a n/a
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 - NDG BMA MAN MAN NAG MAN MAN n/a n/a
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 - YZ0 MAN Z4Y n/a n/a
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 - YZ0 MAN MAN NAG MAN n/a n/a
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 - Z4R MAN n/a n/a
46 3BVU - Z4R MAN MAN n/a n/a
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 - BMA MAN MAN MAN MAN n/a n/a
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 - YZ0 MAN Z4Y NAG MAN n/a n/a
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 - NDG BMA MAN MAN NAG MAN MAN n/a n/a
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 - YZ0 MAN Z4Y n/a n/a
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 - YZ0 MAN MAN NAG MAN n/a n/a
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 - Z4R MAN n/a n/a
46 3BVU - Z4R MAN MAN n/a n/a
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 - BMA MAN MAN MAN MAN n/a n/a
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 - YZ0 MAN Z4Y NAG MAN n/a n/a
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 - NDG BMA MAN MAN NAG MAN MAN n/a n/a
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 - YZ0 MAN Z4Y n/a n/a
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 - YZ0 MAN MAN NAG MAN n/a n/a
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 - Z4R MAN n/a n/a
46 3BVU - Z4R MAN MAN n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NDG BMA MAN MAN NAG MAN MAN; Similar ligands found: 111
No: Ligand ECFP6 Tc MDL keys Tc
1 NDG BMA MAN MAN NAG MAN MAN 1 1
2 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.861702 0.9375
3 NDG BMA MAN MAN NAG GAL NAG 0.83 0.979592
4 NAG NAG BMA MAN MAN NAG GAL NAG 0.821782 0.979592
5 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.805825 1
6 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.795918 0.9375
7 NAG BMA MAN MAN NAG GAL NAG GAL 0.78 0.979592
8 NAG NAG MAN MAN MAN 0.773196 1
9 NAG NAG BMA MAN NAG 0.707071 0.979592
10 YZ0 MAN MAN NAG MAN 0.693069 0.938776
11 NAG BMA MAN MAN MAN MAN 0.69 0.9375
12 BMA MAN MAN NAG GAL NAG 0.654206 1
13 NAG NAG BMA MAN MAN MAN MAN 0.649123 0.923077
14 NAG GAL NAG 0.642105 1
15 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.620968 0.827586
16 C4W NAG FUC BMA MAN MAN NAG 0.609756 0.923077
17 NAG GAL GAL 0.606383 0.9375
18 NAG GAL NAG GAL NAG GAL 0.606061 0.979592
19 NAG GAL NAG GAL 0.606061 1
20 NAG NAG BMA MAN MAN NAG NAG 0.603448 0.90566
21 C4W NAG FUC BMA MAN MAN NAG NAG 0.593496 0.923077
22 BGC GAL NAG NAG GAL GAL 0.592593 1
23 MAN MAN MAN NAG NAG 0.592233 1
24 YZ0 MAN Z4Y NAG MAN 0.581197 0.884615
25 NAG NAG FUL BMA MAN MAN NAG GAL 0.577236 0.90566
26 GDL NAG 0.55914 1
27 NAG GAL BGC GAL 0.554455 0.9375
28 NAG ASN NAG BMA MAN MAN NAG NAG 0.552 0.872727
29 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.552 0.888889
30 1GN ACY GAL 1GN BGC ACY GAL BGC 0.550459 1
31 BGC GAL NAG 0.544554 0.9375
32 NAG GAL 0.543478 0.9375
33 NAG NAG NAG NAG NAG 0.536082 0.979592
34 NAG NAG NAG NAG NAG NAG NAG NAG 0.536082 0.979592
35 NAG NAG NAG NAG NAG NAG 0.536082 0.979592
36 NDG NAG NAG NAG NAG 0.536082 0.979592
37 BGC GAL GLA NGA 0.533333 0.9375
38 NDG GLA GLC NAG GLC RAM 0.528926 0.979592
39 MMA MAN NAG 0.524752 0.938776
40 NAG BMA MAN MAN MAN MAN MAN 0.52381 0.686275
41 MAN BMA MAN MAN MAN MAN MAN 0.513761 0.693878
42 C4W NAG FUC BMA MAN NAG 0.512 0.923077
43 NAG GAL FUC A2G 0.509804 0.958333
44 BMA Z4Y NAG 0.509259 0.918367
45 NDG GLA NAG GLC RAM 0.504132 0.979592
46 NDG NAG GLA NAG GLC RAM 0.504132 0.979592
47 C4W NAG FUC BMA MAN NAG GAL 0.5 0.827586
48 GAL NAG GAL NAG GAL 0.5 1
49 C4W NAG FUC BMA MAN 0.495868 0.923077
50 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.495575 0.62963
51 MAN MAN MAN MAN MAN MAN MAN 0.495327 0.6875
52 BGC GAL NAG GAL FUC 0.486957 0.958333
53 MAN NAG GAL 0.485437 0.9375
54 GLC GAL NAG GAL FUC A2G 0.483607 0.979592
55 MMA MAN NAG MAN NAG NAG 0.482143 0.96
56 NAG GAL FUC GLA 0.481818 0.958333
57 BMA MAN MAN MAN MAN 0.481132 0.693878
58 NAG G6S 0.480769 0.71875
59 A2G GAL NAG 0.476636 1
60 BGC GAL NAG GAL 0.476636 0.9375
61 BMA MAN NAG 0.47619 0.9375
62 BGC GAL NGA 0.475728 0.9375
63 MAN MAN NAG 0.471698 0.9
64 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.46875 0.786885
65 KDO MAN MAN MAN MAN MAN 0.468254 0.653846
66 GAL NAG GAL 0.466667 0.9375
67 BGC BGC BGC BGC 0.466019 0.6875
68 NAG NAG BMA MAN 0.464912 0.923077
69 MMA MAN MAN 0.464646 0.693878
70 BGC GAL GLA NGA GAL 0.459459 0.9375
71 BGC GAL NAG GAL FUC FUC 0.458333 0.938776
72 BGC FUC GAL NAG GAL 0.457627 0.958333
73 BGC FUC GAL NAG 0.45614 0.958333
74 BMA NGT MAN MAN 0.452174 0.661017
75 BGC GLC GLC 0.45 0.6875
76 BGC GAL FUC A2G 0.448276 0.958333
77 C4W NAG FUC BMA 0.445378 0.923077
78 NAG GAL NAG GAL SIA 0.445255 0.90566
79 BMA MAN MAN 0.444444 0.6875
80 MAN NAG 0.444444 0.9375
81 GLC GAL NAG GAL FUC GLA 0.442623 0.958333
82 NDG NAG 0.441176 0.979592
83 NAG NAG NAG TMX 0.440367 0.827586
84 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.4375 0.872727
85 GLC GLC GLC GLC GLC 0.432692 0.6875
86 BGC GLC GLC GLC 0.432692 0.6875
87 GAL NAG 0.431373 0.9375
88 SN5 SN5 0.431373 0.826923
89 MAN MAN MAN GLC 0.431373 0.6875
90 BMA MAN MAN MAN 0.429907 0.714286
91 OPM MAN MAN 0.429907 0.618182
92 MBG NAG 0.421569 0.938776
93 A2G NAG 0.421569 1
94 BGC GAL NGA GAL 0.418182 0.9375
95 MBG A2G 0.417476 0.938776
96 NAG FUC GAL FUC A2G 0.416667 0.979592
97 NAG GAL FUC FUC A2G 0.416667 0.979592
98 GYP GZL NAG 0.415254 0.884615
99 NAG GAL UNU 0.412281 0.94
100 NAG NAG BMA 0.410714 0.923077
101 AMU NAG 0.410714 0.96
102 BGC GAL GLA 0.41 0.6875
103 NGA THR GAL NAG 0.409836 0.941176
104 GAL FUC A2G 0.409091 0.958333
105 TVD GAL 0.405941 0.979592
106 GAL 2NA NAG 0.404762 0.833333
107 BGC FUC GAL FUC A2G 0.403361 0.938776
108 BMA BMA BMA BMA GLA 0.401869 0.6875
109 NAG GAL FUC FUC 0.401786 0.938776
110 NDG FUC GAL FUC 0.401786 0.938776
111 A2G THR GAL NAG 0.401639 0.941176
Similar Ligands (3D)
Ligand no: 1; Ligand: NDG BMA MAN MAN NAG MAN MAN; 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 : 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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