Receptor
PDB id Resolution Class Description Source Keywords
2Z8F 1.65 Å NON-ENZYME: TRANSPORT THE GALACTO-N-BIOSE-/LACTO-N-BIOSE I-BINDING PROTEIN (GL-BP) ABC TRANSPORTER FROM BIFIDOBACTERIUM LONGUM IN COMPLEX WITHT ETRAOSE BIFIDOBACTERIUM LONGUM ABC TRANSPORTER MUCIN CORE-1 HUMAN MILK OLIGOSACCHALIDE SBINDING PROTEIN
Ref.: STRUCTURAL AND THERMODYNAMIC ANALYSES OF SOLUTE-BIN PROTEIN FROM BIFIDOBACTERIUM LONGUM SPECIFIC FOR CO DISACCHARIDE AND LACTO-N-BIOSE I. J.BIOL.CHEM. V. 283 13165 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BGC GAL NAG GAL C:1;
D:1;
Valid;
Valid;
none;
none;
Kd = 11 uM
707.632 n/a O=C(N...
MES A:21;
B:22;
Invalid;
Invalid;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NA A:17;
A:18;
B:16;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
ZN A:11;
A:13;
B:12;
B:14;
B:15;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Z8E 1.99 Å NON-ENZYME: TRANSPORT THE GALACTO-N-BIOSE-/LACTO-N-BIOSE I-BINDING PROTEIN (GL-BP) ABC TRANSPORTER FROM BIFIDOBACTERIUM LONGUM IN COMPLEX WITHN -BIOSE BIFIDOBACTERIUM LONGUM ABC TRANSPORTER MUCIN CORE-1 HUMAN MILK OLIGOSACCHALIDE SBINDING PROTEIN
Ref.: STRUCTURAL AND THERMODYNAMIC ANALYSES OF SOLUTE-BIN PROTEIN FROM BIFIDOBACTERIUM LONGUM SPECIFIC FOR CO DISACCHARIDE AND LACTO-N-BIOSE I. J.BIOL.CHEM. V. 283 13165 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 2Z8F Kd = 11 uM BGC GAL NAG GAL n/a n/a
2 2Z8E Ka = 97400000 M^-1 NGA GAL n/a n/a
3 2Z8D Kd = 86.9 nM NAG 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 197 families.
1 2Z8F Kd = 11 uM BGC GAL NAG GAL n/a n/a
2 2Z8E Ka = 97400000 M^-1 NGA GAL n/a n/a
3 2Z8D Kd = 86.9 nM NAG GAL n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 2Z8F Kd = 11 uM BGC GAL NAG GAL n/a n/a
2 2Z8E Ka = 97400000 M^-1 NGA GAL n/a n/a
3 2Z8D Kd = 86.9 nM NAG GAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC GAL NAG GAL; Similar ligands found: 157
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL NAG GAL 1 1
2 BGC GAL GLA NGA GAL 0.942857 1
3 BGC GAL NGA GAL 0.830986 1
4 BGC GAL NAG 0.780822 1
5 BGC GAL NAG GAL FUC 0.768293 0.978261
6 GLC GAL NAG GAL FUC GLA 0.764706 0.978261
7 BGC GAL GLA NGA 0.753247 1
8 BGC GAL GLA 0.716418 0.733333
9 GLC GAL NAG GAL FUC A2G 0.684783 0.918367
10 BGC BGC BGC BGC BGC BGC BGC BGC 0.676056 0.733333
11 NAG GAL GAL 0.666667 1
12 BGC GAL NAG GAL FUC FUC 0.655556 0.957447
13 NAG GAL NAG GAL 0.641975 0.9375
14 NAG GAL NAG GAL NAG GAL 0.641975 0.918367
15 GAL NAG GAL NAG GAL 0.641975 0.9375
16 BGC GAL NAG NAG GAL GAL 0.640449 0.9375
17 BGC GAL NGA 0.615385 1
18 NAG GAL NAG 0.604938 0.9375
19 MGC GAL 0.589041 0.957447
20 1GN ACY GAL 1GN BGC ACY GAL BGC 0.588889 0.9375
21 BGC FUC GAL NAG GAL 0.586957 0.978261
22 GAL NAG GAL 0.580247 1
23 GLC GLC GLC GLC BGC GLC GLC 0.571429 0.733333
24 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.571429 0.733333
25 MAN BMA BMA BMA BMA BMA BMA 0.571429 0.733333
26 BGC GAL GLA NGA GAL SIA 0.568807 0.865385
27 NAG GAL 0.567568 1
28 A2G GAL 0.567568 1
29 GAL NGA A2G 0.5625 0.9375
30 BGC FUC GAL NAG 0.555556 0.978261
31 BGC GAL SIA NGA GAL 0.554545 0.865385
32 GLA NAG GAL FUC 0.545455 0.978261
33 BGC GAL FUC A2G 0.543478 0.978261
34 BMA MAN NAG 0.535714 1
35 NAG NAG BMA MAN 0.532609 0.865385
36 MAN NAG GAL 0.53012 1
37 GAL NAG FUC GAL 0.52809 0.978261
38 NAG NAG BMA MAN NAG 0.521277 0.918367
39 BGC BGC BGC 0.520548 0.733333
40 BGC BGC BGC BGC BGC BGC BGC 0.520548 0.733333
41 BGC BGC BGC BGC BGC 0.520548 0.733333
42 BGC BGC BGC BGC BGC BGC 0.520548 0.733333
43 GLC BGC BGC BGC 0.520548 0.733333
44 GAL NGA GAL SIA 0.518868 0.865385
45 BGC GAL FUC GLA 0.517647 0.755556
46 MAN NAG PO4 NGA PO4 0.516854 0.789474
47 TVD GAL 0.506494 0.918367
48 A2G MBN GAL 0.505747 0.957447
49 NAG BMA MAN MAN MAN MAN 0.505263 1
50 NAG NAG MAN MAN MAN 0.505155 0.9375
51 BGC GAL NAG GAL SIA 0.504348 0.849057
52 A2G SER GAL 0.5 0.882353
53 A2G THR GAL 0.494253 0.882353
54 BGC GAL SIA NGA GAL SIA 0.491228 0.865385
55 NAG BMA MAN MAN NAG GAL NAG GAL 0.490196 0.918367
56 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.49 1
57 GAL A2G MBN 0.488636 0.9375
58 NAG GAL BGC GAL 0.488636 1
59 BGC GLC GLC 0.4875 0.733333
60 MBG NAG 0.4875 0.957447
61 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.485149 1
62 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.484848 0.9
63 NDG BMA MAN MAN NAG GAL NAG 0.481132 0.918367
64 NAG NAG BMA MAN MAN NAG GAL NAG 0.476636 0.918367
65 NDG BMA MAN MAN NAG MAN MAN 0.476636 0.9375
66 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.47619 0.733333
67 BMA BMA BMA BMA GLA 0.47619 0.733333
68 BGC GAL FUC 0.47561 0.755556
69 GLC GAL BGC FUC 0.47561 0.755556
70 GLC GAL EMB GAL MEC 0.474747 0.75
71 NAG GAL FUC GLA 0.473118 0.978261
72 A2G NPO GAL 0.472527 0.714286
73 NAG BMA 0.469136 0.897959
74 BMA BMA BMA BMA 0.469136 0.733333
75 NAG BDP NAG BDP NAG BDP NAG 0.46875 0.9
76 GLC GLC GLC GLC GLC 0.464286 0.733333
77 BGC GLC GLC GLC 0.464286 0.733333
78 SIA GAL NGA GAL 0.463636 0.865385
79 MAN MAN MAN GLC 0.463415 0.733333
80 C4W NAG FUC BMA MAN 0.462264 0.865385
81 NAG FUC GAL 0.45977 0.978261
82 MBG GAL 0.459459 0.73913
83 GAL NGA GAL SIA SIA 0.458333 0.849057
84 GAL NAG GAL FUC FUC 0.458333 0.957447
85 BGC GAL SIA NGA GAL FUC 0.456 0.865385
86 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.454545 0.9375
87 GAL GLA 0.452055 0.733333
88 BMA MAN MAN NAG GAL NAG 0.451923 0.9375
89 GDL NAG 0.451219 0.9375
90 A2G NAG 0.451219 0.9375
91 NAG NAG BMA 0.450549 0.865385
92 A2G GAL NAG 0.450549 0.9375
93 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.448 0.818182
94 GAL NAG GAL FUC 0.447917 0.9375
95 FUC GAL 0.447368 0.733333
96 MBG A2G 0.445783 0.957447
97 MAN NAG 0.444444 1
98 MAN MAN M6P 0.44186 0.611111
99 MGL GAL 0.44 0.73913
100 BGC GAL SIA 0.439252 0.882353
101 NAG FUC 0.439024 0.956522
102 BGC GLA GAL 0.438356 0.733333
103 GLC GLC FRU 0.438202 0.66
104 NAG G6S 0.438202 0.725806
105 NAG GAL FUC A2G 0.438202 0.978261
106 MMA MAN NAG 0.438202 0.957447
107 GAL NAG GAL SIA 0.4375 0.849057
108 BGC BGC BGC BGC 0.436782 0.733333
109 LOG GAL 0.435294 0.803571
110 BGC BGC BGC XYS BGC XYS 0.434783 0.702128
111 BGC FUC GAL 0.433735 0.755556
112 GLC BGC FUC GAL 0.433735 0.755556
113 NAG GAL FUC 0.433333 0.978261
114 G2F SHG BGC BGC 0.432099 0.673469
115 BGC GLC AGL GLC GLC GLC 0.431579 0.93617
116 NAG NAG NAG NAG NAG NAG 0.430233 0.918367
117 NAG NAG NAG NAG NAG NAG NAG NAG 0.430233 0.918367
118 NAG NAG NAG NAG NAG 0.430233 0.918367
119 NDG NAG NAG NAG NAG 0.430233 0.918367
120 ARE 0.427184 0.836735
121 AAO 0.427184 0.836735
122 NDG GAL 0.426829 0.741379
123 BGC BGC BGC BGC XYS BGC XYS BGC BGC 0.425532 0.702128
124 BGC BGC BGC XYS BGC XYS BGC XYS BGC 0.425532 0.702128
125 BGC BGC BGC BGC BGC XYS 0.425532 0.702128
126 BGC FUC GAL FUC A2G 0.424242 0.957447
127 NAG GAL NAG GAL SIA 0.421488 0.849057
128 NAG NAG BMA MAN MAN MAN MAN 0.421053 0.865385
129 GPM GLC 0.419753 0.6
130 BGC GAL SIA NAG 0.418803 0.865385
131 GLC BGC G6D ACI 0.418367 0.836735
132 NDG GLA NAG GLC RAM 0.418182 0.918367
133 NDG NAG GLA NAG GLC RAM 0.418182 0.918367
134 GAL FUC A2G 0.417582 0.978261
135 GLC GLC G6D ACI 0.415842 0.803922
136 BGC 5VQ GAL GLA 0.414634 0.708333
137 MAN BMA BMA 0.414634 0.702128
138 GLA NAG FUC GAL 0.414141 0.957447
139 GAL SIA NGA GAL 0.412281 0.849057
140 GAL SIA NGA GAL SIA 0.412281 0.865385
141 NAG NAG FUL BMA MAN MAN NAG GAL 0.411765 0.849057
142 GLC GLC AC1 0.409639 0.851064
143 BQZ 0.408451 0.666667
144 GLC GLC AGL HMC 0.407767 0.784314
145 GCU BGC 0.407407 0.717391
146 BGC XGP 0.407407 0.611111
147 NDG GLA GLC NAG GLC RAM 0.40708 0.918367
148 BGC BGC XYS GAL 0.406593 0.702128
149 BGC BGC BGC XYS XYS GAL GAL 0.40404 0.702128
150 BGC GAL SIA SIA 0.403361 0.849057
151 NAG BDP 0.402299 0.916667
152 GLC GLC GLC G6D ACI GLC GLC 0.401961 0.836735
153 GLC GLC AGL HMC GLC 0.4 0.803922
154 G2F BGC BGC BGC BGC BGC 0.4 0.66
155 GLC GLC AC1 GLC GLC GLC 0.4 0.803922
156 GLC GLC G6D GLC ACI GLC 0.4 0.803922
157 GLC EDO GLC 0.4 0.702128
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL NAG GAL; Similar ligands found: 1
No: Ligand Similarity coefficient
1 GLC GAL NAG GAL 0.9457
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2Z8E; Ligand: NGA GAL; 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: 2z8e.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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