Receptor
PDB id Resolution Class Description Source Keywords
2J7M 2.3 Å EC: 3.-.-.- CHARACTERIZATION OF A FAMILY 32 CBM CLOSTRIDIUM PERFRINGENS GLYCOSIDE HYDROLASE CARBOHYDRATE BINDING CBM HYDROLASE H-TRISACCHARIDE
Ref.: THE INTERACTION OF A CARBOHYDRATE-BINDING MODULE FROM A CLOSTRIDIUM PERFRINGENS N-ACETYL-BETA-HEXOSAMINIDASE WITH ITS CARBOHYDRATE RECEPTOR J.BIOL.CHEM. V. 281 37748 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1768;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
NDG GAL FUC A:1769;
Valid;
none;
Ka = 1200 M^-1
529.492 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2J1E 2.4 Å EC: 3.-.-.- HIGH RESOLUTION CRYSTAL STRUCTURE OF CBM32 FROM A N-ACETYL- BETA-HEXOSAMINIDASE IN COMPLEX WITH LACNAC CLOSTRIDIUM PERFRINGENS PROTEIN-CARBOHYDRATE INTERACTIONS GLYCOSIDE HYDROLASE CARBOHYDRATE BINDING MODULE HYDROLASE CBM
Ref.: THE INTERACTION OF A CARBOHYDRATE-BINDING MODULE FROM A CLOSTRIDIUM PERFRINGENS N-ACETYL-BETA-HEXOSAMINIDASE WITH ITS CARBOHYDRATE RECEPTOR J.BIOL.CHEM. V. 281 37748 2006
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 2J7M Ka = 1200 M^-1 NDG GAL FUC n/a n/a
2 2J1A Kd = 980 uM GAL C6 H12 O6 C([C@@H]1[....
3 2J1E Ka = 111 M^-1 NDG GAL n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 176 families.
1 2J7M Ka = 1200 M^-1 NDG GAL FUC n/a n/a
2 2J1A Kd = 980 uM GAL C6 H12 O6 C([C@@H]1[....
3 2J1E Ka = 111 M^-1 NDG GAL 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 2 families.
1 4A45 Kd = 294 uM NGA GAL n/a n/a
2 4AAX Kd = 199 uM NGA C8 H15 N O6 CC(=O)N[C@....
3 4A41 Kd = 591 uM GAL C6 H12 O6 C([C@@H]1[....
4 4A44 - TNR C11 H20 N2 O8 CC(=O)N[C@....
5 2J7M Ka = 1200 M^-1 NDG GAL FUC n/a n/a
6 2J1A Kd = 980 uM GAL C6 H12 O6 C([C@@H]1[....
7 2J1E Ka = 111 M^-1 NDG GAL n/a n/a
8 2V72 Ka = 1360 M^-1 GAL C6 H12 O6 C([C@@H]1[....
9 4P5Y Kd = 0.9 mM NGA C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDG GAL FUC; Similar ligands found: 176
No: Ligand ECFP6 Tc MDL keys Tc
1 FUL GAL NAG 1 1
2 DR2 1 1
3 FUC GAL NDG 1 1
4 NDG GAL FUC 1 1
5 FUC GAL NAG 1 1
6 NAG FUC 0.809524 0.956522
7 FUC GAL NAG A2G 0.805195 0.851852
8 GAL NDG FUC FUC 0.739726 0.978723
9 BCW 0.739726 0.978723
10 FUC GAL NAG FUC 0.739726 0.978723
11 GAL NAG FUC FUC 0.739726 0.978723
12 FUC NAG GAL FUC 0.739726 0.978723
13 FUC NDG GAL FUC 0.739726 0.978723
14 FUC GAL NDG FUC 0.739726 0.978723
15 BDZ 0.739726 0.978723
16 NAG GAL FUC 0.712329 1
17 DR3 0.712329 1
18 A2G GAL NAG FUC 0.703704 0.938776
19 FUC GAL GLC 0.695652 0.73913
20 FUC LAT 0.695652 0.73913
21 GLC GAL FUC 0.695652 0.73913
22 BGC GAL FUC 0.695652 0.73913
23 LAT FUC 0.695652 0.73913
24 GAL NDG 0.671642 0.978261
25 NLC 0.671642 0.978261
26 NDG GAL 0.671642 0.978261
27 FUC GAL MAG FUC 0.649351 0.958333
28 FUC GAL NAG GAL BGC 0.62069 1
29 FUC GAL NAG GAL FUC 0.619048 0.978723
30 GAL NDG FUC 0.597403 1
31 FUC NDG GAL 0.597403 1
32 GAL NAG FUC 0.597403 1
33 FUC NAG GAL 0.597403 1
34 CBS 0.597222 0.958333
35 NAG NDG 0.597222 0.958333
36 NAG GDL 0.597222 0.958333
37 CBS CBS 0.597222 0.958333
38 BGC GAL NAG GAL FUC FUC 0.593407 0.978723
39 GLC GAL NAG GAL FUC FUC 0.593407 0.978723
40 MAN BMA NAG 0.592105 0.978261
41 NAG GAL GAL 0.592105 0.978261
42 GLA GAL NAG 0.592105 0.978261
43 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.576087 0.978261
44 A2G GAL BGC FUC 0.568182 1
45 NAG NAG NDG 0.565789 0.938776
46 NDG NAG NAG 0.565789 0.938776
47 NDG NAG NAG NAG 0.565789 0.938776
48 NAG NAG NAG 0.565789 0.938776
49 NAG NAG NAG NAG NAG 0.565789 0.938776
50 NDG NAG NAG NDG 0.565789 0.938776
51 CTO 0.565789 0.938776
52 NDG NAG NAG NDG NAG 0.565789 0.938776
53 NAG NAG NAG NDG 0.565789 0.938776
54 NAG NAG NAG NAG 0.565789 0.938776
55 NAG NAG NAG NAG NAG NAG NAG NAG 0.565789 0.938776
56 NAG NAG NAG NAG NDG NAG 0.565789 0.938776
57 NAG NAG NAG NAG NDG 0.565789 0.938776
58 NAG NAG NAG NAG NAG NAG 0.565789 0.938776
59 FUC NAG 0.561644 0.978261
60 XYS GAL FUC 0.551282 0.723404
61 G6S NAG 0.55 0.75
62 MAN BMA NAG NAG MAN NAG GAL GAL 0.541667 0.938776
63 NAG MAN GAL BMA NDG MAN NAG GAL 0.541667 0.938776
64 NAG MAN MAN MAN NAG GAL NAG GAL 0.541667 0.938776
65 NAG MAN GAL BMA NAG MAN NAG GAL 0.541667 0.938776
66 NAG GAL NAG 0.536585 0.958333
67 NAG GAL GAL NAG 0.535714 0.958333
68 GAL NAG GAL NAG GAL NAG 0.535714 0.938776
69 FUC GAL NAG NON FUC 0.531915 0.836364
70 GAL BGC NAG GAL 0.53012 0.978261
71 A2G GAL FUC 0.52439 1
72 NGA GAL FUC 0.52439 1
73 A2G GLA FUC 0.52439 1
74 BGC GLA GAL FUC 0.52439 0.73913
75 FUC GAL A2G 0.52439 1
76 FUC GL0 A2G 0.52439 1
77 FUC GLA A2G 0.52439 1
78 FUC GAL NAG A2G FUC 0.521739 0.938776
79 NAG GAL FUC FUC A2G 0.521739 0.938776
80 NAG BMA NAG MAN MAN NAG NAG 0.520408 0.938776
81 MAG FUC GAL 0.518519 0.958333
82 NAG MAN BMA NDG MAN NAG GAL 0.514852 0.938776
83 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.514563 0.958333
84 FUC GAL 0.514286 0.717391
85 CTO TMX 0.511905 0.793103
86 TCG 0.511905 0.793103
87 M5G 0.509804 0.958333
88 BGC FUC GAL FUC A2G 0.505495 0.978723
89 GLC FUC GAL FUC A2G 0.505495 0.978723
90 GLA GAL NAG FUC GAL GLC 0.505155 1
91 GLA NAG GAL FUC 0.5 1
92 HS2 0.5 0.86
93 GAL NAG GAL FUC 0.5 1
94 FUC BGC GAL NAG GAL 0.494737 1
95 NAG BMA MAN MAN MAN MAN 0.494505 0.978261
96 BHE 0.493827 0.648148
97 FUC BGC GAL 0.493506 0.73913
98 UNU GAL NAG 0.488636 0.9
99 4YA 0.4875 0.648148
100 FUC BHG 0.4875 0.648148
101 BHG FUC 0.4875 0.648148
102 GAL NAG MAN 0.481928 0.978261
103 MAN NAG GAL 0.481928 0.978261
104 A2G GAL NAG FUC GAL GLC 0.480392 0.938776
105 GLC GAL NAG GAL FUC A2G 0.480392 0.938776
106 FUC BGC GAL NAG 0.478261 1
107 GCS GCS NAG 0.477273 0.918367
108 8VZ 0.473684 0.938776
109 NAG NAG NAG NAG NAG NAG NAG 0.472527 0.851852
110 FUC NAG TA5 0.47191 0.681818
111 SN5 SN5 0.468354 0.823529
112 ASG 0.465753 0.650794
113 NAG NAG BMA MAN MAN 0.463918 0.958333
114 MAN MAN NAG MAN NAG 0.463918 0.958333
115 NAG MAN GAL MAN MAN NAG GAL 0.463918 0.958333
116 FUC NAG GLA GAL 0.462366 0.978723
117 GAL GAL FUC 0.461538 0.73913
118 FUC GAL GLA 0.461538 0.73913
119 FUC GLA GLA 0.461538 0.73913
120 GLA GLA FUC 0.461538 0.73913
121 GLA GAL FUC 0.461538 0.73913
122 MAN MAN BMA 0.459459 0.717391
123 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.459184 0.92
124 GAL A2G 0.454545 0.978261
125 GAL NGA 0.454545 0.978261
126 A2G GAL 0.454545 0.978261
127 NGA GAL BGC 0.452381 0.978261
128 GAL NGA A2G 0.451219 0.938776
129 MAN MAN NAG 0.448276 0.9375
130 G4S MAG FUC 0.445652 0.725806
131 GLC GAL NAG GAL 0.444444 0.978261
132 BEK GAL NAG 0.443299 0.807018
133 NAG MAN MMA 0.44186 0.978723
134 BMA MAN MAN 0.441558 0.717391
135 NAG MAN MAN MAN NAG 0.44086 0.958333
136 LAT NAG GAL 0.438202 0.978261
137 GAL NAG GAL BGC 0.438202 0.978261
138 BGC GAL NAG GAL 0.438202 0.978261
139 FUC NAG T45 0.4375 0.671642
140 BGA 0.43299 0.836364
141 MAN NAG 0.43038 0.978261
142 NAG MAN BMA 0.426966 0.978261
143 NAG MAN MAN 0.426966 0.978261
144 NDG NAG 0.426829 0.938776
145 NAG 0.426471 0.869565
146 HSQ 0.426471 0.869565
147 NDG 0.426471 0.869565
148 NGA 0.426471 0.869565
149 A2G 0.426471 0.869565
150 BM3 0.426471 0.869565
151 SGA MAG FUC 0.425532 0.725806
152 NAG GAL SIA 0.424528 0.867925
153 4U1 0.424528 0.884615
154 M6P MAN MAN 0.423529 0.6
155 GAL NGA GLA BGC GAL 0.419355 0.978261
156 GAL MGC 0.417722 0.978723
157 NAG GAL GAL NAG GAL 0.417582 0.958333
158 NAG GAL BGC 0.41573 0.978261
159 MAN MAN MAN GLC 0.414634 0.717391
160 MBG A2G 0.414634 0.978723
161 A2G MBG 0.414634 0.978723
162 NAG GCU NAG GCD 0.411215 0.851852
163 FUC GAL NGA 0.411111 0.93617
164 GAL NAG GAL 0.411111 0.9375
165 NGA GLA GAL BGC 0.408602 0.978261
166 NAG MUB 0.406593 0.92
167 NAG NAG BMA 0.406593 0.884615
168 NAG AMU 0.406593 0.92
169 NAG NDG BMA 0.406593 0.884615
170 GLA MBG 0.402778 0.723404
171 NAG A2G 0.402439 0.958333
172 NAG BMA 0.402439 0.88
173 NAG NGA 0.402439 0.958333
174 MMA MAN NAG MAN NAG NAG 0.402062 0.92
175 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.401869 0.9
176 4U2 0.4 0.901961
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2J1E; Ligand: NDG GAL; Similar sites found: 15
This union binding pocket(no: 1) in the query (biounit: 2j1e.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O4N TPV 0.0125 0.43022 None
2 3S43 478 0.02377 0.4112 None
3 1PFY MSP 0.01392 0.42216 3.33333
4 2NSX IFM 0.01355 0.40757 3.33333
5 4UFH GIF 0.009791 0.40458 4.66667
6 4U63 FAD 0.03453 0.40186 5.33333
7 2ZAT NAP 0.0181 0.42833 6
8 2IFB PLM 0.01505 0.40497 6.10687
9 1EOM NAG MAN MAN MAN NAG GAL NAG GAL 0.02698 0.40354 6.66667
10 5F7R GLC GLC 0.0277 0.40028 7.33333
11 2UVJ ADA ADA ADA 0.02421 0.40266 8
12 3AGC RCC 0.02579 0.41417 8.66667
13 3L9R L9R 0.04413 0.4052 10.2041
14 3EQO LGC 0.007496 0.42064 11.3333
15 4BTI 7R9 0.01666 0.41938 16.6667
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