Receptor
PDB id Resolution Class Description Source Keywords
5KKB 1.77 Å EC: 3.2.1.113 STRUCTURE OF MOUSE GOLGI ALPHA-1,2-MANNOSIDASE IA AND MAN9GL COMPLEX MUS MUSCULUS ALPHA/ALPHA BARREL GOLGI APPARATUS DEGLYCOSYLATION GLYCANSUBSTRATE ANALOG SUGAR BINDING PROTEIN
Ref.: SUBSTRATE RECOGNITION AND CATALYSIS BY GH47 ALPHA-MANNOSIDASES INVOLVED IN ASN-LINKED GLYCAN MA IN THE MAMMALIAN SECRETORY PATHWAY. PROC. NATL. ACAD. SCI. V. 113 E7890 2016 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BU1 B:713;
Invalid;
none;
submit data
90.121 C4 H10 O2 C(CCO...
1PS B:711;
A:712;
Invalid;
Invalid;
none;
none;
submit data
201.243 C8 H11 N O3 S c1cc[...
NAG A:710;
B:710;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
BMA NAG MAN MAN MAN MAN MAN MAN MAN B:701;
A:701;
Valid;
Valid;
none;
none;
submit data
1518.34 n/a O=C(N...
LA B:712;
A:711;
Valid;
Valid;
none;
none;
submit data
138.905 La [La+3...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KKB 1.77 Å EC: 3.2.1.113 STRUCTURE OF MOUSE GOLGI ALPHA-1,2-MANNOSIDASE IA AND MAN9GL COMPLEX MUS MUSCULUS ALPHA/ALPHA BARREL GOLGI APPARATUS DEGLYCOSYLATION GLYCANSUBSTRATE ANALOG SUGAR BINDING PROTEIN
Ref.: SUBSTRATE RECOGNITION AND CATALYSIS BY GH47 ALPHA-MANNOSIDASES INVOLVED IN ASN-LINKED GLYCAN MA IN THE MAMMALIAN SECRETORY PATHWAY. PROC. NATL. ACAD. SCI. V. 113 E7890 2016 U.S.A.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5KKB - BMA NAG MAN MAN MAN MAN MAN MAN MAN n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5KKB - BMA NAG MAN MAN MAN MAN MAN MAN MAN n/a n/a
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5KKB - BMA NAG MAN MAN MAN MAN MAN MAN MAN n/a n/a
2 2RI9 Ki = 0.6 mM MMA LDY n/a n/a
3 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
4 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
5 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
6 5KK7 - SMD C13 H24 O10 S CO[C@@H]1[....
7 1DL2 - NDG NAG NDG BMA MAN MAN MAN MAN n/a n/a
8 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
9 1X9D Kd = 110 uM SMD C13 H24 O10 S CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BMA NAG MAN MAN MAN MAN MAN MAN MAN; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 BMA NAG MAN MAN MAN MAN MAN MAN MAN 1 1
2 NAG BMA MAN MAN MAN MAN 0.869048 1
3 M5G 0.861702 0.9375
4 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.824742 0.9375
5 NAG MAN MAN MAN NAG GAL NAG GAL 0.760417 0.918367
6 MAN BMA NAG NAG MAN NAG GAL GAL 0.760417 0.918367
7 NAG MAN GAL BMA NDG MAN NAG GAL 0.760417 0.918367
8 NAG MAN GAL BMA NAG MAN NAG GAL 0.760417 0.918367
9 MAN MAN NAG MAN NAG 0.752688 0.9375
10 NAG NAG BMA MAN MAN 0.752688 0.9375
11 NAG MAN BMA NDG MAN NAG GAL 0.722772 0.918367
12 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.676471 0.918367
13 NAG NAG BMA MAN MAN MAN MAN 0.672897 0.865385
14 NAG BMA NAG MAN MAN NAG NAG 0.666667 0.918367
15 MAN BMA NAG 0.651163 1
16 NAG GAL GAL 0.651163 1
17 GLA GAL NAG 0.651163 1
18 GAL BGC NAG GAL 0.608696 1
19 NDG GAL 0.60241 1
20 NLC 0.60241 1
21 GAL NDG 0.60241 1
22 NAG GAL GAL NAG 0.595745 0.9375
23 GAL NAG GAL NAG GAL NAG 0.595745 0.918367
24 WZ5 0.588235 0.957447
25 NAG MAN GAL MAN MAN NAG GAL 0.582524 0.9375
26 FUL GAL NAG 0.576087 0.978261
27 DR2 0.576087 0.978261
28 NDG GAL FUC 0.576087 0.978261
29 FUC GAL NAG 0.576087 0.978261
30 FUC GAL NDG 0.576087 0.978261
31 MAN MAN MAN BMA MAN MAN MAN 0.575758 0.73913
32 NAG BMA MAN MAN MAN MAN MAN 0.572917 0.693878
33 MAN MAN MAN BMA MAN 0.569892 0.733333
34 1GN ACY GAL ACY 1GN BGC GAL BGC 0.568627 0.9375
35 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.568627 0.9375
36 MAN MAN MAN MAN 0.561798 0.733333
37 MAN MAN BMA MAN 0.561798 0.733333
38 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.553398 0.666667
39 NAG GAL NAG 0.547368 0.9375
40 M5S 0.538462 0.733333
41 MAN BMA MAN MAN MAN 0.538462 0.733333
42 KDO MAN MAN MAN MAN MAN 0.530435 0.693878
43 G6S NAG 0.526316 0.762712
44 FUC GAL NAG GAL BGC 0.514019 0.978261
45 NAG NAG BMA MAN MAN NAG NAG 0.512821 0.849057
46 GLC GAL NAG GAL 0.51 1
47 GLC GAL NAG GAL FUC FUC 0.495495 0.957447
48 BGC GAL NAG GAL FUC FUC 0.495495 0.957447
49 FUC GAL NAG A2G 0.495327 0.833333
50 MAN MMA MAN 0.494505 0.73913
51 WZ4 0.491525 0.9
52 NAG MAN MAN MAN NAG 0.490385 0.9375
53 BGC GAL NAG GAL 0.49 1
54 GAL NAG GAL BGC 0.49 1
55 LAT NAG GAL 0.49 1
56 NAG GAL GAL NAG GAL 0.485149 0.9375
57 OPM MAN MAN 0.484536 0.653846
58 NAG FUC 0.483516 0.934783
59 BMA NGT MAN MAN 0.476636 0.696429
60 GLC GLC GLC BGC 0.473684 0.733333
61 MAN MAN MAN GLC 0.473118 0.733333
62 GAL NGA GLA BGC GAL 0.471154 1
63 MAN NAG GAL 0.469388 1
64 GAL NAG MAN 0.469388 1
65 ASN NAG NAG BMA MAN MAN NAG NAG 0.464567 0.833333
66 CBS CBS 0.462366 0.9375
67 GLC GLC GLC GLC 0.462366 0.733333
68 CBS 0.462366 0.9375
69 NAG NDG 0.462366 0.9375
70 NAG GDL 0.462366 0.9375
71 NAG GAL BGC 0.455446 1
72 GLC GLC GLC GLC GLC GLC 0.452632 0.733333
73 GLA GAL NAG FUC GAL GLC 0.452174 0.978261
74 GAL NAG FUC FUC 0.45098 0.957447
75 FUC NAG GAL FUC 0.45098 0.957447
76 FUC NDG GAL FUC 0.45098 0.957447
77 BCW 0.45098 0.957447
78 FUC GAL NDG FUC 0.45098 0.957447
79 FUC GAL NAG FUC 0.45098 0.957447
80 NAG MAN BMA 0.45098 1
81 GAL NDG FUC FUC 0.45098 0.957447
82 BDZ 0.45098 0.957447
83 NAG MAN MAN 0.45098 1
84 BMA MAN MAN 0.450549 0.733333
85 NGA GLA GAL BGC 0.447619 1
86 8VZ 0.445652 0.918367
87 DR3 0.445545 0.978261
88 NAG GAL FUC 0.445545 0.978261
89 A2G GAL NAG FUC 0.445455 0.918367
90 WZ3 0.444444 0.723404
91 NAG NAG NAG NAG NAG NAG NAG NAG 0.443299 0.918367
92 NDG NAG NAG NAG 0.443299 0.918367
93 NAG NAG NAG NAG NAG 0.443299 0.918367
94 NAG NAG NAG NAG 0.443299 0.918367
95 NDG NAG NAG NDG NAG 0.443299 0.918367
96 NAG NAG NAG 0.443299 0.918367
97 NAG NAG NDG 0.443299 0.918367
98 NAG NAG NAG NDG 0.443299 0.918367
99 NAG NAG NAG NAG NDG NAG 0.443299 0.918367
100 NAG NAG NAG NAG NAG NAG 0.443299 0.918367
101 NDG NAG NAG 0.443299 0.918367
102 CTO 0.443299 0.918367
103 NAG NAG NAG NAG NDG 0.443299 0.918367
104 NDG NAG NAG NDG 0.443299 0.918367
105 FUC BGC GAL NAG GAL 0.442478 0.978261
106 BMA BMA GLA BMA BMA 0.438776 0.733333
107 NAG NAG BMA MAN 0.436364 0.865385
108 GLA GAL BGC 0.434783 0.733333
109 GLA GAL GAL 0.434783 0.733333
110 UNU GAL NAG 0.433962 0.918367
111 MAN MAN BMA 0.433333 0.733333
112 GAL NGA 0.430108 1
113 A2G GAL 0.430108 1
114 GAL A2G 0.430108 1
115 GAL NGA A2G 0.428571 0.918367
116 NAG NAG BMA MAN NAG 0.428571 0.849057
117 HS2 0.425743 0.877551
118 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.42446 0.833333
119 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.42446 0.833333
120 TCG 0.423077 0.775862
121 CTO TMX 0.423077 0.775862
122 NAG MAN MMA 0.421569 0.957447
123 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.421429 0.833333
124 M6P MAN MAN 0.42 0.611111
125 BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.733333
126 BGC BGC BGC BGC 0.416667 0.733333
127 MAN MAN MAN MAN MAN MAN MAN MAN 0.415929 0.647059
128 MAN MAN MAN 0.41573 0.733333
129 GLC GLC GLC GLC GLC BGC 0.41573 0.733333
130 GLC GLC GLC GLC BGC 0.41573 0.733333
131 GLC GLC GLC 0.41573 0.733333
132 FUC GAL NAG GAL FUC 0.414414 0.957447
133 GAL NAG FUC 0.411765 0.978261
134 FUC NAG GAL 0.411765 0.978261
135 FUC NDG GAL 0.411765 0.978261
136 GAL NDG FUC 0.411765 0.978261
137 GLC GAL NAG GAL FUC A2G 0.409836 0.918367
138 4U1 0.409836 0.865385
139 NAG GAL SIA 0.409836 0.849057
140 A2G GAL NAG FUC GAL GLC 0.409836 0.918367
141 GAL NAG GAL 0.409524 0.957447
142 GLA BGC 0.409091 0.733333
143 GLA BMA 0.409091 0.733333
144 LAK 0.409091 0.733333
145 GLA GLC 0.409091 0.733333
146 BGC GLA 0.409091 0.733333
147 BMA GLA 0.409091 0.733333
148 MAN BMA 0.409091 0.733333
149 MLB 0.409091 0.733333
150 GAL GAL 0.409091 0.733333
151 FUC LAT 0.408163 0.755556
152 GLC GAL FUC 0.408163 0.755556
153 FUC GAL GLC 0.408163 0.755556
154 BGC GAL FUC 0.408163 0.755556
155 LAT FUC 0.408163 0.755556
156 MAN H1M MAN 0.405941 0.693878
Ligand no: 2; Ligand: LA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LA 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KKB; Ligand: LA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5kkb.bio1) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KKB; Ligand: BMA NAG MAN MAN MAN MAN MAN MAN MAN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5kkb.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KKB; Ligand: LA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5kkb.bio2) has 4 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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