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...
LA B:712;
A:711;
 Valid;
Valid;
 none;
none;
 submit data
138.905 La [La+3...
NAG BMA MAN MAN MAN MAN MAN MAN MAN D:1;
C:1;
 Valid;
Valid;
 none;
none;
 submit data
1518.34 n/a O=C(N...
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 6 families.
1 5KKB - LA La [La+3]
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5KKB - LA La [La+3]
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5KKB - LA La [La+3]
2 2RI9 Ki = 0.6 mM MMA LDY n/a n/a
3 1KRE - DMJ C6 H13 N O4 C1[C@H]([C....
4 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
5 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
6 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
7 5KK7 - Z5L MAN n/a n/a
8 1DL2 - NAG NDG BMA MAN MAN MAN MAN n/a n/a
9 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
10 1X9D Kd = 110 uM Z5L MAN n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LA 1 1
Ligand no: 2; Ligand: NAG BMA MAN MAN MAN MAN MAN MAN MAN; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA MAN MAN MAN MAN MAN MAN MAN 1 1
2 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.91954 1
3 NDG BMA MAN MAN NAG MAN MAN 0.861702 0.9375
4 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.824742 0.9375
5 NAG BMA MAN MAN NAG GAL NAG GAL 0.760417 0.918367
6 NAG NAG MAN MAN MAN 0.752688 0.9375
7 NAG BMA MAN MAN MAN MAN 0.73913 1
8 NDG BMA MAN MAN NAG GAL NAG 0.722772 0.918367
9 NAG NAG BMA MAN MAN NAG GAL NAG 0.715686 0.918367
10 NAG NAG BMA MAN MAN MAN MAN 0.672897 0.865385
11 NAG GAL GAL 0.651163 1
12 NAG GAL BGC GAL 0.608696 1
13 NAG GAL 0.60241 1
14 NAG NAG BMA MAN NAG 0.6 0.918367
15 NAG GAL NAG GAL 0.595745 0.9375
16 NAG GAL NAG GAL NAG GAL 0.595745 0.918367
17 YZ0 MAN MAN NAG MAN 0.588235 0.957447
18 BGC GAL NAG NAG GAL GAL 0.582524 0.9375
19 NAG GAL FUC A2G 0.576087 0.978261
20 MAN BMA MAN MAN MAN MAN MAN 0.575758 0.73913
21 NAG BMA MAN MAN MAN MAN MAN 0.572917 0.693878
22 MAN MAN MAN MAN MAN MAN MAN 0.572917 0.733333
23 1GN ACY GAL 1GN BGC ACY GAL BGC 0.568627 0.9375
24 BMA MAN MAN NAG GAL NAG 0.555556 0.9375
25 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.553398 0.666667
26 NAG GAL NAG 0.547368 0.9375
27 NAG NAG FUL BMA MAN MAN NAG GAL 0.541667 0.849057
28 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.536 0.775862
29 KDO MAN MAN MAN MAN MAN 0.530435 0.693878
30 NAG G6S 0.526316 0.725806
31 NAG GAL FUC GLA 0.524752 0.978261
32 BGC GAL NAG GAL FUC 0.514019 0.978261
33 NAG NAG BMA MAN MAN NAG NAG 0.512821 0.849057
34 C4W NAG FUC BMA MAN MAN NAG 0.512 0.865385
35 BMA MAN MAN MAN MAN 0.510204 0.73913
36 C4W NAG FUC BMA MAN MAN NAG NAG 0.508065 0.865385
37 BGC GAL NAG GAL FUC FUC 0.495495 0.957447
38 BGC BGC BGC BGC 0.494737 0.733333
39 MMA MAN MAN 0.494505 0.73913
40 BGC GLC GLC 0.494505 0.733333
41 YZ0 MAN Z4Y NAG MAN 0.491525 0.9
42 MAN MAN MAN NAG NAG 0.490385 0.9375
43 BGC GAL NAG GAL 0.49 1
44 GAL NAG GAL NAG GAL 0.485149 0.9375
45 OPM MAN MAN 0.484536 0.653846
46 BMA NGT MAN MAN 0.476636 0.696429
47 GLC GLC GLC GLC GLC 0.473684 0.733333
48 BGC GLC GLC GLC 0.473684 0.733333
49 MAN MAN MAN GLC 0.473118 0.733333
50 BMA MAN MAN 0.472527 0.733333
51 BGC GAL GLA NGA GAL 0.471154 1
52 C4W NAG FUC BMA MAN 0.470085 0.865385
53 MAN NAG GAL 0.469388 1
54 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.468254 0.833333
55 NAG ASN NAG BMA MAN MAN NAG NAG 0.468254 0.818182
56 GDL NAG 0.462366 0.9375
57 BGC GAL NAG 0.455446 1
58 NDG GLA GLC NAG GLC RAM 0.454545 0.918367
59 BMA MAN MAN MAN 0.454545 0.723404
60 GLC GAL NAG GAL FUC GLA 0.452174 0.978261
61 C4W NAG FUC BMA MAN NAG GAL 0.451613 0.775862
62 NDG FUC GAL FUC 0.45098 0.957447
63 NAG GAL FUC FUC 0.45098 0.957447
64 GAL NAG GAL 0.45 1
65 BGC GAL GLA NGA 0.447619 1
66 A2G GAL NAG 0.446602 0.9375
67 TVD GAL 0.445652 0.918367
68 NAG GAL FUC 0.445545 0.978261
69 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.445255 0.818182
70 NDG NAG NAG NAG NAG 0.443299 0.918367
71 NAG NAG NAG NAG NAG NAG NAG NAG 0.443299 0.918367
72 NAG NAG NAG NAG NAG NAG 0.443299 0.918367
73 NAG NAG NAG NAG NAG 0.443299 0.918367
74 BGC FUC GAL NAG GAL 0.442478 0.978261
75 BMA BMA BMA BMA GLA 0.438776 0.733333
76 NAG NAG BMA MAN 0.436364 0.865385
77 BGC GAL GLA 0.434783 0.733333
78 NAG GAL UNU 0.433962 0.918367
79 NAG GAL NAG GAL SIA 0.431818 0.849057
80 A2G GAL 0.430108 1
81 C4W NAG FUC BMA 0.429825 0.865385
82 NDG NAG GLA NAG GLC RAM 0.429752 0.918367
83 NDG GLA NAG GLC RAM 0.429752 0.918367
84 C4W NAG FUC BMA MAN NAG 0.428571 0.865385
85 BGC GAL NGA GAL 0.427184 1
86 NAG NAG NAG TMX 0.423077 0.775862
87 MMA MAN NAG 0.421569 0.957447
88 GLC GLC GLC 0.418367 0.702128
89 GLA NAG GAL FUC 0.416667 0.978261
90 BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.733333
91 MAN MAN MAN MAN MAN MAN MAN MAN 0.415929 0.647059
92 BGC GLC GLC GLC GLC GLC 0.41573 0.733333
93 BGC GLC GLC GLC GLC 0.41573 0.733333
94 GAL NAG GAL FUC FUC 0.414414 0.957447
95 BMA Z4Y NAG 0.412844 0.978261
96 MAN MAN MAN 0.411765 0.717391
97 NAG FUC GAL 0.411765 0.978261
98 NAG NAG 0.41 0.918367
99 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.41 0.733333
100 GLC GAL NAG GAL FUC A2G 0.409836 0.918367
101 BGC GAL FUC 0.408163 0.755556
102 GLC GAL BGC FUC 0.408163 0.755556
103 NAG GCS GCS 0.407407 0.918367
104 H1M MAN MAN 0.405941 0.693878
105 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.403727 0.737705
Similar Ligands (3D)
Ligand no: 1; Ligand: LA; Similar ligands found: 7
No: Ligand Similarity coefficient
1 RU 1.0000
2 AM 1.0000
3 ZCM 1.0000
4 4PU 1.0000
5 CD 1.0000
6 F 1.0000
7 YB 1.0000
Ligand no: 2; Ligand: NAG BMA MAN MAN MAN MAN MAN 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 : 5KKB; Ligand: LA; 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: 5kkb.bio1) has 4 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KKB; Ligand: LA; Similar sites found with APoc: 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 4 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KKB; Ligand: NAG BMA MAN MAN MAN MAN MAN MAN MAN; Similar sites found with APoc: 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 31 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback