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 E:1;
H:1;
F:1;
B:1;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
Atoms found LESS than expected: % Diff = 0.014;
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 552 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 426 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 322 families.
1 5SWB Kd = 0.962 uM NAG BMA MAN MAN MAN MAN n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG BMA MAN MAN MAN MAN; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA MAN MAN MAN MAN 1 1
2 NAG NAG MAN MAN MAN 0.764045 0.9375
3 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.73913 1
4 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.731183 1
5 NAG GAL GAL 0.721519 1
6 NDG BMA MAN MAN NAG MAN MAN 0.69 0.9375
7 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.676471 0.9375
8 NAG BMA MAN MAN NAG GAL NAG GAL 0.663265 0.918367
9 NAG GAL 0.649351 1
10 NAG GAL NAG GAL NAG GAL 0.636364 0.918367
11 NAG GAL NAG GAL 0.636364 0.9375
12 NDG BMA MAN MAN NAG GAL NAG 0.631068 0.918367
13 NAG NAG BMA MAN MAN NAG GAL NAG 0.625 0.918367
14 BGC GAL NAG NAG GAL GAL 0.602041 0.9375
15 NAG GAL BGC GAL 0.595506 1
16 NAG GAL NAG 0.58427 0.9375
17 NAG G6S 0.561798 0.725806
18 1GN ACY GAL 1GN BGC ACY GAL BGC 0.555556 0.9375
19 NAG NAG BMA MAN MAN MAN MAN 0.517544 0.865385
20 GAL NAG GAL NAG GAL 0.515789 0.9375
21 MMA MAN MAN 0.511628 0.73913
22 NAG GAL FUC GLA 0.510204 0.978261
23 NAG NAG BMA MAN NAG 0.509804 0.918367
24 BGC GAL NAG GAL 0.505263 1
25 NAG NAG FUL BMA MAN MAN NAG GAL 0.504202 0.849057
26 BGC BGC BGC BGC 0.494505 0.733333
27 GDL NAG 0.494253 0.9375
28 BGC GAL GLA NGA GAL 0.484848 1
29 C4W NAG FUC BMA MAN 0.482143 0.865385
30 BMA MAN MAN MAN MAN 0.479167 0.73913
31 NAG GAL FUC A2G 0.478723 0.978261
32 GAL NAG GAL 0.478723 1
33 TVD GAL 0.476744 0.918367
34 C4W NAG FUC BMA MAN MAN NAG 0.475806 0.865385
35 BMA NGT MAN MAN 0.475728 0.696429
36 NAG NAG BMA MAN 0.475728 0.865385
37 A2G GAL NAG 0.474227 0.9375
38 BMA MAN MAN NAG GAL NAG 0.472727 0.9375
39 NAG NAG NAG NAG NAG NAG NAG NAG 0.472527 0.918367
40 NAG NAG NAG NAG NAG NAG 0.472527 0.918367
41 NAG NAG NAG NAG NAG 0.472527 0.918367
42 NDG NAG NAG NAG NAG 0.472527 0.918367
43 BMA MAN MAN 0.471264 0.733333
44 BGC GAL NAG 0.46875 1
45 MAN NAG GAL 0.468085 1
46 BGC GAL GLA 0.465116 0.733333
47 NAG BMA MAN MAN MAN MAN MAN 0.464646 0.693878
48 BGC GLC GLC 0.460674 0.733333
49 BGC GAL GLA NGA 0.46 1
50 A2G GAL 0.45977 1
51 YZ0 MAN MAN NAG MAN 0.457944 0.957447
52 BGC FUC GAL NAG GAL 0.453704 0.978261
53 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.453125 0.775862
54 BMA MAN MAN MAN 0.452632 0.723404
55 NAG GAL NAG GAL SIA 0.452381 0.849057
56 NAG NAG NAG TMX 0.44898 0.775862
57 NAG GAL UNU 0.445545 0.918367
58 BGC BGC BGC BGC BGC BGC BGC BGC 0.444444 0.733333
59 MAN BMA MAN MAN MAN MAN MAN 0.442308 0.73913
60 GLC GLC GLC GLC GLC 0.44086 0.733333
61 BGC GLC GLC GLC 0.44086 0.733333
62 BGC GAL NGA GAL 0.438776 1
63 NAG NAG BMA MAN MAN NAG NAG 0.436975 0.849057
64 GLC U8V 0.435294 0.76087
65 BGC GAL NAG GAL FUC 0.431193 0.978261
66 NDG GLA GLC NAG GLC RAM 0.428571 0.918367
67 NDG NAG GLA NAG GLC RAM 0.42735 0.918367
68 NDG GLA NAG GLC RAM 0.42735 0.918367
69 C4W NAG FUC BMA 0.427273 0.865385
70 MAN AML MAN MAN MAN MAN MAN MAN MAN 0.425926 0.666667
71 C4W NAG FUC BMA MAN MAN NAG NAG 0.425197 0.865385
72 GLC GAL NAG GAL FUC GLA 0.424779 0.978261
73 NAG FUC GAL 0.42268 0.978261
74 MAN MAN MAN 0.42268 0.717391
75 NAG NAG 0.421053 0.918367
76 GLC BGC BGC BGC 0.418605 0.733333
77 BGC BGC BGC BGC BGC BGC BGC 0.418605 0.733333
78 BGC BGC BGC 0.418605 0.733333
79 BGC BGC BGC BGC BGC 0.418605 0.733333
80 BGC BGC BGC BGC BGC BGC 0.418605 0.733333
81 NAG GAL 5N6 0.418033 0.833333
82 BGC GAL NAG GAL FUC FUC 0.415929 0.957447
83 NAG NAG BMA 0.415842 0.865385
84 NGA THR GAL NAG 0.414414 0.882353
85 NAG BMA 0.413043 0.897959
86 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.411765 0.818182
87 MGC GAL 0.411111 0.957447
88 GAL NAG 0.408602 1
89 MAN MAN MAN MAN MAN MAN MAN 0.407767 0.733333
90 MAN MAN M6P 0.40625 0.611111
91 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.40625 0.733333
92 BMA BMA BMA BMA GLA 0.40625 0.733333
93 MAN MAN MAN NAG NAG 0.40566 0.9375
94 YZ0 MAN Z4Y NAG MAN 0.404959 0.9
95 NAG GAL PKM 0.404959 0.849057
96 NAG GCS GCS 0.403846 0.918367
97 C4W NAG FUC BMA MAN NAG GAL 0.403226 0.775862
98 NAG GAL SIA 0.401709 0.865385
99 MBG GAL 0.4 0.73913
100 BMA MAN NAG 0.4 1
101 GLC GLC GLC 0.4 0.702128
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG BMA 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 : 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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