Receptor
PDB id Resolution Class Description Source Keywords
5SWB 1.73 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF N-GLYCAN TRANSPORT SOLUTE BINDING PROTE FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH MAN5GLCNAC STREPTOCOCCUS PNEUMONIAE SOLUTE BINDING PROTEIN PROTEIN-GLYCAN COMPLEX ALPHA/BETA DHYDROLASE
Ref.: MOLECULAR CHARACTERIZATION OF N-GLYCAN DEGRADATION TRANSPORT IN STREPTOCOCCUS PNEUMONIAE AND ITS CONTR TO VIRULENCE. PLOS PATHOG. V. 13 06090 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD A:510;
A:513;
A:512;
A:517;
D:509;
G:508;
C:516;
A:511;
D:508;
A:508;
C:510;
G:513;
G:512;
D:510;
A:507;
A:516;
G:510;
A:509;
C:515;
C:514;
G:509;
C:507;
A:514;
A:515;
C:509;
C:508;
C:512;
D:501;
G:511;
D:512;
G:507;
C:513;
D:511;
C:511;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
112.411 Cd [Cd+2...
NAG BMA MAN MAN MAN MAN D:502;
A:501;
C:501;
G:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
Kd = 0.962 uM
1017.89 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5SWB 1.73 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF N-GLYCAN TRANSPORT SOLUTE BINDING PROTE FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH MAN5GLCNAC STREPTOCOCCUS PNEUMONIAE SOLUTE BINDING PROTEIN PROTEIN-GLYCAN COMPLEX ALPHA/BETA DHYDROLASE
Ref.: MOLECULAR CHARACTERIZATION OF N-GLYCAN DEGRADATION TRANSPORT IN STREPTOCOCCUS PNEUMONIAE AND ITS CONTR TO VIRULENCE. PLOS PATHOG. V. 13 06090 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5SWB Kd = 0.962 uM NAG BMA 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 391 families.
1 5SWB Kd = 0.962 uM NAG BMA MAN MAN MAN MAN n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 5SWB Kd = 0.962 uM NAG BMA MAN MAN MAN MAN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG BMA MAN MAN MAN MAN; Similar ligands found: 124
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA MAN MAN MAN MAN 1 1
2 NAG NAG BMA MAN MAN 0.764045 0.9375
3 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.73913 1
4 MAN BMA NAG 0.721519 1
5 GLA GAL NAG 0.721519 1
6 M5G 0.69 0.9375
7 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.676471 0.9375
8 MAN BMA NAG NAG MAN NAG GAL GAL 0.663265 0.918367
9 NAG MAN MAN MAN NAG GAL NAG GAL 0.663265 0.918367
10 NLC 0.649351 1
11 GAL NDG 0.649351 1
12 NDG GAL 0.649351 1
13 NAG GAL GAL NAG 0.636364 0.9375
14 GAL NAG GAL NAG GAL NAG 0.636364 0.918367
15 NAG MAN BMA NDG MAN NAG GAL 0.631068 0.918367
16 NAG NAG BMA MAN MAN NAG GAL NAG 0.625 0.918367
17 GAL BGC NAG GAL 0.595506 1
18 NAG GAL NAG 0.58427 0.9375
19 NAG BMA NAG MAN MAN NAG NAG 0.576923 0.918367
20 G6S NAG 0.561798 0.725806
21 1GN ACY GAL ACY 1GN BGC GAL BGC 0.555556 0.9375
22 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.555556 0.9375
23 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.542056 0.918367
24 LAT NAG GAL 0.526316 1
25 GLC GAL NAG GAL 0.526316 1
26 NAG NAG BMA MAN MAN MAN MAN 0.517544 0.865385
27 NAG GAL GAL NAG GAL 0.515789 0.9375
28 MAN MMA MAN 0.511628 0.73913
29 MAN MAN MAN MAN 0.511364 0.733333
30 MAN MAN BMA MAN 0.511364 0.733333
31 MAN BMA MAN MAN MAN 0.505618 0.733333
32 M5S 0.505618 0.733333
33 GAL NAG GAL GLC 0.505263 1
34 BGC GAL NAG GAL 0.505263 1
35 NAG NAG FUL BMA MAN MAN NAG GAL 0.504202 0.849057
36 NAG FUC 0.5 0.934783
37 NAG GDL 0.494253 0.9375
38 NDG NAG 0.494253 0.9375
39 CBS CBS 0.494253 0.9375
40 CBS 0.494253 0.9375
41 MAN MAN MAN BMA MAN 0.489362 0.733333
42 GAL NGA GLA BGC GAL 0.484848 1
43 FUC C4W NAG BMA MAN 0.482143 0.865385
44 GAL NAG GAL BGC 0.48 0.957447
45 NDG GAL FUC 0.478723 0.978261
46 NAG GAL FUC 0.478723 0.978261
47 FUL GAL NAG 0.478723 0.978261
48 GAL NAG FUC 0.478723 0.978261
49 DR2 0.478723 0.978261
50 FUC GAL NAG 0.478723 0.978261
51 FUC GAL NDG 0.478723 0.978261
52 8VZ 0.476744 0.918367
53 FUC C4W NAG BMA MAN MAN NAG 0.475806 0.865385
54 BMA NGT MAN MAN 0.475728 0.696429
55 NAG NAG BMA MAN 0.475728 0.865385
56 NAG A2G GAL 0.474227 0.9375
57 WZ3 0.473118 0.723404
58 NAG MAN BMA MAN NAG GAL 0.472727 0.9375
59 NAG NAG NDG NAG 0.472527 0.918367
60 NDG NAG NAG NDG 0.472527 0.918367
61 NAG NAG NAG NAG NAG 0.472527 0.918367
62 NAG NAG NAG NAG NDG 0.472527 0.918367
63 CTO 0.472527 0.918367
64 NDG NAG NAG 0.472527 0.918367
65 NDG NAG NAG NAG 0.472527 0.918367
66 NAG NAG NAG NDG 0.472527 0.918367
67 NAG NAG NAG NAG NAG NAG 0.472527 0.918367
68 NAG NAG NDG 0.472527 0.918367
69 NAG NAG NAG NAG NAG NAG NAG NAG 0.472527 0.918367
70 MAN BMA MAN 0.471264 0.733333
71 NAG GAL BGC 0.46875 1
72 GAL NAG MAN 0.468085 1
73 GLA GAL GAL 0.465116 0.733333
74 NAG BMA MAN MAN MAN MAN MAN 0.464646 0.693878
75 NGA GLA GAL BGC 0.46 1
76 GAL NGA 0.45977 1
77 GAL A2G 0.45977 1
78 A2G GAL 0.45977 1
79 WZ5 0.457944 0.957447
80 FUC BGC GAL NAG GAL 0.453704 0.978261
81 TCG 0.44898 0.775862
82 UNU GAL NAG 0.445545 0.918367
83 BGC BGC BGC BGC BGC BGC BGC BGC 0.444444 0.733333
84 MAN MAN MAN BMA MAN MAN MAN 0.442308 0.73913
85 GLC GLC GLC BGC 0.44086 0.733333
86 HS2 0.4375 0.877551
87 NAG NAG BMA MAN MAN NAG NAG 0.436975 0.849057
88 GAL NAG GAL 0.434343 0.957447
89 GLC NAG GAL GAL FUC 0.431193 0.978261
90 FUC GAL NAG GAL BGC 0.431193 0.978261
91 GAL GLC NAG GAL FUC 0.431193 0.978261
92 4U1 0.431034 0.865385
93 NAG GAL SIA 0.431034 0.849057
94 A2G GAL NAG FUC 0.429907 0.918367
95 FUC GAL NAG A2G 0.429907 0.918367
96 FUC C4W NAG BMA 0.427273 0.865385
97 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.425926 0.666667
98 FUC C4W NAG BMA MAN MAN NAG NAG 0.425197 0.865385
99 GLA GAL NAG FUC GAL GLC 0.424779 0.978261
100 FUC NDG GAL 0.42268 0.978261
101 GAL NDG FUC 0.42268 0.978261
102 P3M 0.419355 0.6
103 GLC BGC BGC BGC BGC BGC BGC 0.418605 0.733333
104 BGC BGC BGC GLC BGC BGC 0.418605 0.733333
105 GLC GAL NAG GAL FUC FUC 0.415929 0.957447
106 BGC GAL NAG GAL FUC FUC 0.415929 0.957447
107 NAG NDG BMA 0.415842 0.865385
108 NAG NAG BMA 0.415842 0.865385
109 NAG BMA 0.413043 0.897959
110 BMA MAN MAN MAN MAN 0.412371 0.733333
111 GAL MGC 0.411111 0.957447
112 4U2 0.408696 0.882353
113 MAN MAN MAN MAN MAN MAN MAN 0.407767 0.733333
114 BMA BMA GLA BMA BMA 0.40625 0.733333
115 NAG MAN MAN 0.405941 1
116 NAG MAN MAN MAN NAG 0.40566 0.9375
117 WZ4 0.404959 0.9
118 GCS GCS NAG 0.403846 0.918367
119 NAG SIA GAL 0.401709 0.865385
120 NAG NAG BMA MAN NAG 0.401709 0.849057
121 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.40146 0.833333
122 GAL MBG 0.4 0.73913
123 MDM 0.4 0.73913
124 M13 0.4 0.73913
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5SWB; Ligand: NAG BMA 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: 1) in the query (biounit: 5swb.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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