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 = 0.014;
none;
Kd = 0.962 uM
1031.91 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 473 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 355 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 272 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: 175
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA MAN MAN MAN MAN 1 1
2 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.869048 1
3 NAG NAG BMA MAN MAN 0.855422 0.9375
4 MAN MAN NAG MAN NAG 0.855422 0.9375
5 M5G 0.804348 0.9375
6 NAG GAL GAL 0.75 1
7 MAN BMA NAG 0.75 1
8 GLA GAL NAG 0.75 1
9 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.731959 0.9375
10 NAG MAN GAL BMA NDG MAN NAG GAL 0.684211 0.918367
11 MAN BMA NAG NAG MAN NAG GAL GAL 0.684211 0.918367
12 NAG MAN MAN MAN NAG GAL NAG GAL 0.684211 0.918367
13 NAG MAN GAL BMA NAG MAN NAG GAL 0.684211 0.918367
14 NDG GAL 0.675676 1
15 GAL NDG 0.675676 1
16 NLC 0.675676 1
17 NAG GAL GAL NAG 0.658824 0.9375
18 GAL NAG GAL NAG GAL NAG 0.658824 0.918367
19 NAG MAN BMA NDG MAN NAG GAL 0.65 0.918367
20 GAL BGC NAG GAL 0.635294 1
21 MAN MAN MAN MAN 0.625 0.733333
22 MAN MAN BMA MAN 0.625 0.733333
23 1GN ACY GAL ACY 1GN BGC GAL BGC 0.623656 0.9375
24 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.623656 0.9375
25 MAN BMA MAN MAN MAN 0.617284 0.733333
26 M5S 0.617284 0.733333
27 NAG GAL NAG 0.604651 0.9375
28 NAG BMA NAG MAN MAN NAG NAG 0.594059 0.918367
29 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.588235 0.918367
30 G6S NAG 0.581395 0.762712
31 NAG NAG BMA MAN MAN MAN MAN 0.574074 0.865385
32 MAN MMA MAN 0.567901 0.73913
33 GLC GAL NAG GAL 0.543478 1
34 MAN MAN MAN BMA MAN 0.539326 0.733333
35 BMA NGT MAN MAN 0.536082 0.696429
36 NAG GAL GAL NAG GAL 0.532609 0.9375
37 GLC GLC GLC GLC 0.53012 0.733333
38 GAL NAG GAL BGC 0.521739 1
39 BGC GAL NAG GAL 0.521739 1
40 LAT NAG GAL 0.521739 1
41 NAG FUC 0.518072 0.934783
42 WZ5 0.514852 0.957447
43 CBS CBS 0.511905 0.9375
44 NAG GDL 0.511905 0.9375
45 CBS 0.511905 0.9375
46 NAG NDG 0.511905 0.9375
47 NAG MAN GAL MAN MAN NAG GAL 0.509804 0.9375
48 GLC GLC GLC BGC 0.505747 0.733333
49 WZ3 0.505618 0.723404
50 GAL NGA GLA BGC GAL 0.5 1
51 NAG BMA MAN MAN MAN MAN MAN 0.494737 0.693878
52 DR2 0.494505 0.978261
53 FUL GAL NAG 0.494505 0.978261
54 FUC GAL NDG 0.494505 0.978261
55 FUC GAL NAG 0.494505 0.978261
56 NDG GAL FUC 0.494505 0.978261
57 8VZ 0.493976 0.918367
58 NAG NAG BMA MAN 0.49 0.865385
59 NAG NAG NAG NDG 0.488636 0.918367
60 NDG NAG NAG NAG 0.488636 0.918367
61 NAG NAG NAG NAG NAG 0.488636 0.918367
62 NAG NAG NAG NAG 0.488636 0.918367
63 NAG NAG NAG NAG NDG 0.488636 0.918367
64 NAG NAG NAG 0.488636 0.918367
65 NDG NAG NAG NDG NAG 0.488636 0.918367
66 NAG NAG NAG NAG NAG NAG NAG NAG 0.488636 0.918367
67 NAG NAG NAG NAG NAG NAG 0.488636 0.918367
68 NAG NAG NAG NAG NDG NAG 0.488636 0.918367
69 NAG NAG NDG 0.488636 0.918367
70 NDG NAG NAG 0.488636 0.918367
71 CTO 0.488636 0.918367
72 NDG NAG NAG NDG 0.488636 0.918367
73 MAN MAN MAN BMA MAN MAN MAN 0.484848 0.73913
74 NAG GAL BGC 0.483871 1
75 GAL NAG MAN 0.483516 1
76 MAN NAG GAL 0.483516 1
77 GLA GAL BGC 0.481928 0.733333
78 GLA GAL GAL 0.481928 0.733333
79 GAL NGA 0.47619 1
80 A2G GAL 0.47619 1
81 GAL A2G 0.47619 1
82 NGA GLA GAL BGC 0.474227 1
83 GAL NGA A2G 0.47191 0.918367
84 BMA BMA GLA BMA BMA 0.466667 0.733333
85 FUC BGC GAL NAG GAL 0.466667 0.978261
86 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.466019 0.666667
87 GLC GLC GLC GLC GLC GLC 0.465909 0.733333
88 TCG 0.463158 0.775862
89 CTO TMX 0.463158 0.775862
90 BGC BGC BGC BGC BGC BGC BGC BGC 0.45977 0.733333
91 BGC BGC BGC BGC 0.45977 0.733333
92 UNU GAL NAG 0.459184 0.918367
93 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.453846 0.833333
94 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.453846 0.833333
95 HS2 0.451613 0.877551
96 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.450382 0.833333
97 NAG NAG BMA MAN MAN NAG NAG 0.448276 0.849057
98 GAL NAG GAL 0.447917 0.957447
99 MAN H1M MAN 0.445652 0.693878
100 MAN MAN MAN 0.444444 0.733333
101 GLC GLC GLC 0.444444 0.733333
102 GLC GLC GLC GLC BGC 0.444444 0.733333
103 GLC GLC GLC GLC GLC BGC 0.444444 0.733333
104 FUC GAL NAG GAL BGC 0.443396 0.978261
105 NAG GAL SIA 0.442478 0.849057
106 4U1 0.442478 0.865385
107 A2G GAL NAG FUC 0.442308 0.918367
108 KDO MAN MAN MAN MAN MAN 0.439655 0.693878
109 GAL GAL 0.4375 0.733333
110 GLA BGC 0.4375 0.733333
111 BGC GLA 0.4375 0.733333
112 MLB 0.4375 0.733333
113 GLA GLC 0.4375 0.733333
114 GLA BMA 0.4375 0.733333
115 MAN BMA 0.4375 0.733333
116 LAK 0.4375 0.733333
117 BMA GLA 0.4375 0.733333
118 GLA GAL NAG FUC GAL GLC 0.436364 0.978261
119 GAL NDG FUC 0.43617 0.978261
120 FUC NAG GAL 0.43617 0.978261
121 GAL NAG FUC 0.43617 0.978261
122 FUC NDG GAL 0.43617 0.978261
123 GCS GCS NAG 0.434343 0.9375
124 GLC BGC BGC BGC 0.433735 0.733333
125 BGC BGC BGC BGC BGC 0.433735 0.733333
126 BGC BGC BGC 0.433735 0.733333
127 GLC BGC BGC BGC BGC BGC BGC 0.433735 0.733333
128 BGC BGC BGC GLC BGC BGC 0.433735 0.733333
129 BGC BGC BGC ASO BGC BGC ASO 0.433735 0.733333
130 P3M 0.433333 0.6
131 NAG NDG BMA 0.428571 0.865385
132 NAG NAG BMA 0.428571 0.865385
133 WZ4 0.42735 0.9
134 GLC GAL NAG GAL FUC FUC 0.427273 0.957447
135 BGC GAL NAG GAL FUC FUC 0.427273 0.957447
136 NAG BMA 0.426966 0.897959
137 GAL MGC 0.425287 0.957447
138 FUC GAL NAG A2G 0.424528 0.833333
139 4U2 0.419643 0.882353
140 NAG MAN BMA 0.418367 1
141 NAG MAN MAN 0.418367 1
142 NAG NAG NAG NAG NAG NAG NAG 0.417476 0.833333
143 NAG MAN MAN MAN NAG 0.417476 0.9375
144 SIA GAL NAG 0.412281 0.865385
145 NAG SIA GAL 0.412281 0.865385
146 NAG NAG BMA MAN NAG 0.412281 0.849057
147 NGA GAL BGC 0.410526 1
148 GLC BGC 0.407407 0.733333
149 GLA GLA 0.407407 0.733333
150 BGC GLC 0.407407 0.733333
151 CBK 0.407407 0.733333
152 MAL 0.407407 0.733333
153 GAL GLC 0.407407 0.733333
154 CBI 0.407407 0.733333
155 GAL BGC 0.407407 0.733333
156 BGC BMA 0.407407 0.733333
157 LAT 0.407407 0.733333
158 GLA GAL 0.407407 0.733333
159 BMA BMA 0.407407 0.733333
160 MAL MAL 0.407407 0.717391
161 BEK GAL NAG 0.407407 0.789474
162 GLC GAL 0.407407 0.733333
163 MAB 0.407407 0.733333
164 B2G 0.407407 0.733333
165 LBT 0.407407 0.733333
166 BGC GAL 0.407407 0.733333
167 BMA GAL 0.407407 0.733333
168 N9S 0.407407 0.733333
169 MAN MAN MAN GLC 0.406593 0.733333
170 SN5 SN5 0.406593 0.803922
171 U63 0.404762 0.673469
172 ASN NAG NAG BMA MAN MAN NAG NAG 0.404762 0.833333
173 BGC BGC GLC 0.402299 0.733333
174 8VW 0.401869 0.849057
175 GLA EGA 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: 11
This union binding pocket(no: 1) in the query (biounit: 5swb.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NE7 16G 0.01943 0.41558 2.07612
2 5MRH Q9Z 0.01696 0.41433 2.31092
3 5F7U GLC GLC 0.02833 0.41029 3.15126
4 1H0A I3P 0.02446 0.41416 3.16456
5 2WBV SIA 0.004763 0.45872 3.7037
6 1KZL CRM 0.005888 0.43318 4.32692
7 4RF7 ARG 0.02791 0.40007 4.83193
8 4ONT SIA GAL BGC 0.01624 0.42317 5.99369
9 4DS0 A2G GAL NAG FUC 0.006331 0.42309 6.74847
10 2J0B UDP 0.02276 0.41868 13.2143
11 5W3X ACO 0.01509 0.42428 21.25
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