Receptor
PDB id Resolution Class Description Source Keywords
3BVW 1.2 Å EC: 3.2.1.114 GOLGI MANNOSIDASE II D204A CATALYTIC NUCLEOPHILE MUTANT COMP METHYL (2-DEOXY-2-ACETAMIDO-BETA-D-GLUCOPYRANOSYL)-(1->2)-AM ANNOPYRANOSYL- (1->3)-[ALPHA-D-MANNOPYRANOSYL-(1->6)-6-THIMA NNOPYRANOSYL- (1->6)]-BETA-D-MANNOPYRANOSIDE DROSOPHILA MELANOGASTER FAMILY 38 GLYCOYSL HYDROLASE 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
MPD A:1102;
Invalid;
none;
submit data
118.174 C6 H14 O2 C[C@@...
ZN A:1101;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
YZ0 MAN Z4Y NAG MAN B:1;
Valid;
none;
submit data
899.867 n/a S(CC1...
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: YZ0 MAN Z4Y NAG MAN; Similar ligands found: 43
No: Ligand ECFP6 Tc MDL keys Tc
1 YZ0 MAN Z4Y NAG MAN 1 1
2 YZ0 MAN MAN NAG MAN 0.773196 0.94
3 MMA MAN NAG 0.614583 0.94
4 NDG BMA MAN MAN NAG MAN MAN 0.581197 0.884615
5 MAN MAN MAN NAG NAG 0.542056 0.884615
6 NDG BMA MAN MAN NAG GAL NAG 0.533333 0.867925
7 MMA MAN NAG MAN NAG NAG 0.53211 0.886792
8 NAG NAG BMA MAN MAN NAG GAL NAG 0.528926 0.867925
9 BMA MAN MAN NAG GAL NAG 0.521368 0.884615
10 NAG BMA MAN MAN MAN MAN MAN 0.518868 0.692308
11 MBG NAG 0.505155 0.94
12 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.496296 0.741935
13 C4W NAG FUC BMA MAN MAN NAG NAG 0.492424 0.821429
14 NAG BMA MAN MAN NAG GAL NAG GAL 0.491667 0.867925
15 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.491525 0.9
16 MMA MAN MAN 0.489796 0.7
17 NAG NAG BMA MAN MAN MAN MAN 0.488189 0.821429
18 GYP GZL NAG 0.486726 0.886792
19 NAG NAG BMA MAN MAN NAG NAG 0.484127 0.807018
20 BMA MAN MAN MAN 0.480769 0.72
21 C4W NAG FUC BMA MAN MAN NAG 0.474074 0.821429
22 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.472441 0.884615
23 BMA Z4Y NAG 0.464286 0.92
24 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.46281 0.9
25 NAG ASN NAG BMA MAN MAN NAG NAG 0.455224 0.779661
26 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.455224 0.793103
27 NAG NAG MAN MAN MAN 0.453782 0.884615
28 MAN MAN NAG 0.453704 0.865385
29 NAG NAG BMA MAN NAG 0.452991 0.867925
30 U1Y BGC 0.447917 0.76
31 MBG A2G 0.441176 0.94
32 NAG NAG FUL BMA MAN MAN NAG GAL 0.433824 0.807018
33 MAN BMA MAN MAN MAN MAN MAN 0.431034 0.7
34 1GN ACY GAL 1GN BGC ACY GAL BGC 0.428571 0.884615
35 C4W NAG FUC BMA MAN NAG 0.428571 0.821429
36 NDG GLA GLC NAG GLC RAM 0.419847 0.867925
37 BGC GAL NAG NAG GAL GAL 0.418033 0.884615
38 NDG NAG GLA NAG GLC RAM 0.407692 0.867925
39 NDG GLA NAG GLC RAM 0.407692 0.867925
40 C4W NAG FUC BMA MAN NAG GAL 0.407407 0.741935
41 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.404959 0.607143
42 NAG BMA MAN MAN MAN MAN 0.404959 0.9
43 MAN MAN MAN MAN MAN MAN MAN 0.4 0.66
Similar Ligands (3D)
Ligand no: 1; Ligand: YZ0 MAN Z4Y NAG 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
APoc FAQ
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