Receptor
PDB id Resolution Class Description Source Keywords
6EQ8 2.19 Å NON-ENZYME: BINDING STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN (PBP) MELB (ATU COMPLEX WITH GALACTINOL FROM AGROBACTERIUM FABRUM C58 RHIZOBIUM RADIOBACTER TRANSPORT PROTEIN
Ref.: THE PLANT DEFENSE SIGNAL GALACTINOL IS SPECIFICALLY A NUTRIENT BY THE BACTERIAL PATHOGENAGROBACTERIUM F J. BIOL. CHEM. V. 293 7930 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA C:717;
A:720;
D:709;
C:715;
A:721;
C:714;
A:718;
B:709;
B:707;
A:719;
B:708;
C:716;
A:717;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
CL B:712;
D:719;
B:711;
C:724;
C:737;
C:735;
B:720;
D:717;
D:715;
C:730;
B:718;
D:720;
C:726;
C:725;
D:716;
A:725;
B:714;
B:719;
C:734;
C:732;
C:728;
A:726;
D:721;
B:717;
C:729;
B:713;
C:733;
A:727;
B:721;
B:716;
B:715;
C:736;
C:731;
A:728;
D:718;
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;
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;
none;
submit data
35.453 Cl [Cl-]
EDO A:705;
A:702;
A:708;
A:707;
C:702;
A:715;
A:713;
A:706;
D:706;
A:711;
C:704;
B:702;
C:709;
D:701;
B:705;
C:703;
C:711;
A:709;
A:704;
C:707;
A:714;
C:706;
D:704;
A:710;
C:710;
C:708;
D:702;
A:701;
C:701;
B:704;
D:705;
B:703;
C:705;
B:701;
D:707;
A:712;
A:703;
C:712;
D:703;
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;
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;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
PEG D:711;
C:721;
D:710;
D:712;
A:722;
C:718;
C:720;
B:710;
C:719;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
PG4 C:723;
D:714;
A:724;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
194.226 C8 H18 O5 C(COC...
BQZ A:716;
B:706;
C:713;
D:708;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 0.12 uM
342.296 C12 H22 O11 C([C@...
P4G A:723;
D:713;
C:722;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
162.227 C8 H18 O3 CCOCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6EQ8 2.19 Å NON-ENZYME: BINDING STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN (PBP) MELB (ATU COMPLEX WITH GALACTINOL FROM AGROBACTERIUM FABRUM C58 RHIZOBIUM RADIOBACTER TRANSPORT PROTEIN
Ref.: THE PLANT DEFENSE SIGNAL GALACTINOL IS SPECIFICALLY A NUTRIENT BY THE BACTERIAL PATHOGENAGROBACTERIUM F J. BIOL. CHEM. V. 293 7930 2018
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 6EQ0 Kd = 24 uM GLA C6 H12 O6 C([C@@H]1[....
2 6EQ8 Kd = 0.12 uM BQZ C12 H22 O11 C([C@@H]1[....
3 6EQ1 Kd = 24.6 uM STW C24 H42 O21 C([C@@H]1[....
4 6EPZ Kd = 0.76 uM MLB C12 H22 O11 C([C@@H]1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 6EQ0 Kd = 24 uM GLA C6 H12 O6 C([C@@H]1[....
2 6EQ8 Kd = 0.12 uM BQZ C12 H22 O11 C([C@@H]1[....
3 6EQ1 Kd = 24.6 uM STW C24 H42 O21 C([C@@H]1[....
4 6EPZ Kd = 0.76 uM MLB C12 H22 O11 C([C@@H]1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 6EQ0 Kd = 24 uM GLA C6 H12 O6 C([C@@H]1[....
2 6EQ8 Kd = 0.12 uM BQZ C12 H22 O11 C([C@@H]1[....
3 6EQ1 Kd = 24.6 uM STW C24 H42 O21 C([C@@H]1[....
4 6EPZ Kd = 0.76 uM MLB C12 H22 O11 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BQZ; Similar ligands found: 223
No: Ligand ECFP6 Tc MDL keys Tc
1 BQZ 1 1
2 TRE 0.675676 0.909091
3 MAN GLC 0.644444 0.909091
4 LB2 0.644444 0.909091
5 NGR 0.644444 0.909091
6 M3M 0.644444 0.909091
7 GLA MBG 0.622222 0.857143
8 LAT GLA 0.622222 0.909091
9 2M4 0.622222 0.909091
10 MDM 0.617021 0.857143
11 M13 0.617021 0.857143
12 GAL MBG 0.617021 0.857143
13 BGC BMA 0.608696 0.909091
14 MAB 0.608696 0.909091
15 LAT 0.608696 0.909091
16 GAL BGC 0.608696 0.909091
17 CBI 0.608696 0.909091
18 CBK 0.608696 0.909091
19 BGC GAL 0.608696 0.909091
20 B2G 0.608696 0.909091
21 LBT 0.608696 0.909091
22 MAL 0.608696 0.909091
23 N9S 0.608696 0.909091
24 GLA GLA 0.608696 0.909091
25 GLC GAL 0.608696 0.909091
26 GLA GAL 0.608696 0.909091
27 BMA GAL 0.608696 0.909091
28 DR5 0.583333 0.857143
29 MMA MAN 0.583333 0.857143
30 GLC BGC BGC BGC BGC BGC BGC 0.58 0.909091
31 BGC BGC BGC GLC BGC BGC 0.58 0.909091
32 DOM 0.571429 0.857143
33 GLA GAL GAL 0.566038 0.909091
34 MYG 0.565217 0.789474
35 BGC BGC BGC BGC 0.56 0.909091
36 BMA BMA BMA BMA BMA BMA 0.56 0.909091
37 CE8 0.56 0.909091
38 MAN BMA BMA 0.56 0.909091
39 BGC GLC GLC GLC GLC 0.56 0.909091
40 DXI 0.56 0.909091
41 MLR 0.56 0.909091
42 MT7 0.56 0.909091
43 GLC BGC BGC BGC BGC 0.56 0.909091
44 BGC BGC GLC 0.56 0.909091
45 GAL GAL GAL 0.56 0.909091
46 CT3 0.56 0.909091
47 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.56 0.909091
48 CTT 0.56 0.909091
49 GLA GAL GLC 0.56 0.909091
50 GAL FUC 0.56 0.909091
51 CEY 0.56 0.909091
52 B4G 0.56 0.909091
53 BGC GLC GLC GLC 0.56 0.909091
54 MAN BMA BMA BMA BMA 0.56 0.909091
55 BGC BGC BGC BGC BGC BGC 0.56 0.909091
56 GLC BGC BGC 0.56 0.909091
57 BMA BMA BMA BMA BMA 0.56 0.909091
58 MAN BMA BMA BMA BMA BMA 0.56 0.909091
59 GLC BGC GLC 0.56 0.909091
60 GLC GLC BGC 0.56 0.909091
61 BGC BGC BGC 0.56 0.909091
62 MAN MAN BMA BMA BMA BMA 0.56 0.909091
63 GLC GLC GLC GLC GLC 0.56 0.909091
64 BGC GLC GLC 0.56 0.909091
65 CEX 0.56 0.909091
66 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.56 0.909091
67 BGC GLC GLC GLC GLC GLC GLC 0.56 0.909091
68 CE5 0.56 0.909091
69 BGC BGC BGC BGC BGC 0.56 0.909091
70 GLC BGC BGC BGC BGC BGC 0.56 0.909091
71 CTR 0.56 0.909091
72 GLC GAL GAL 0.56 0.909091
73 MTT 0.56 0.909091
74 BMA MAN BMA 0.56 0.909091
75 BGC BGC BGC GLC 0.56 0.909091
76 GLA GAL BGC 0.56 0.909091
77 BMA BMA BMA 0.56 0.909091
78 CE6 0.56 0.909091
79 GLC BGC BGC BGC 0.56 0.909091
80 RZM 0.55102 0.659091
81 GLA EGA 0.54902 0.857143
82 CGC 0.54717 0.909091
83 BMA BMA 0.54 0.882353
84 BGC BGC 0.54 0.882353
85 MAL EDO 0.538462 0.857143
86 BMA BMA MAN 0.538462 0.909091
87 MAN MAN BMA 0.538462 0.909091
88 U63 0.529412 0.810811
89 MAN MNM 0.528302 0.638298
90 BMA MAN MAN MAN 0.527273 0.909091
91 BGC BGC BGC BGC BGC BGC BGC BGC 0.526316 0.909091
92 5QP 0.519231 0.909091
93 FRU GAL 0.519231 0.763158
94 BMA FRU 0.519231 0.763158
95 MVP 0.518519 0.666667
96 MAN BMA MAN 0.517857 0.909091
97 MAN MAN MAN GLC 0.517241 0.909091
98 BMA IFM 0.509434 0.681818
99 9MR 0.509434 0.714286
100 BGC OXZ 0.509434 0.638298
101 IFM BMA 0.509434 0.681818
102 IFM BGC 0.509434 0.681818
103 GDQ GLC 0.509091 0.638298
104 FMO 0.5 0.789474
105 NOY BGC 0.5 0.638298
106 MBG 0.5 0.878788
107 GAL GAL SO4 0.5 0.6
108 GLA GAL BGC 5VQ 0.5 0.810811
109 MMA 0.5 0.878788
110 AMG 0.5 0.878788
111 MAN MMA MAN 0.5 0.857143
112 GAL MGC 0.5 0.638298
113 GLC DMJ 0.5 0.666667
114 GYP 0.5 0.878788
115 NOJ GLC 0.5 0.666667
116 ABL 0.490909 0.638298
117 MAN DGO 0.490566 0.882353
118 T6P 0.490196 0.697674
119 MAN G63 0.482143 0.625
120 MAN 7D1 0.480769 0.857143
121 MAN MAN MAN MAN 0.47541 0.909091
122 MAN MAN BMA MAN 0.47541 0.909091
123 GLA GAL GLC NBU 0.474576 0.769231
124 G2F BGC BGC BGC BGC BGC 0.474576 0.789474
125 A2G GAL 0.473684 0.666667
126 NLC 0.473684 0.666667
127 NDG GAL 0.473684 0.666667
128 GAL A2G 0.473684 0.666667
129 GAL NDG 0.473684 0.666667
130 GAL NGA 0.473684 0.666667
131 8VZ 0.473684 0.612245
132 MAN BMA MAN MAN MAN 0.467742 0.909091
133 M5S 0.467742 0.909091
134 BGC BGC BGC FRU 0.466667 0.789474
135 BTU 0.462963 0.763158
136 TUR 0.462963 0.763158
137 GLC FRU 0.462963 0.763158
138 LSE 0.460317 0.625
139 G2I 0.459016 0.697674
140 LMT 0.459016 0.714286
141 UMQ 0.459016 0.714286
142 G3I 0.459016 0.697674
143 OXZ BGC BGC 0.459016 0.625
144 LMU 0.459016 0.714286
145 GLC GLC XYP 0.459016 0.909091
146 DMU 0.459016 0.714286
147 GAL GAL FUC 0.457627 0.882353
148 GLA GLA FUC 0.457627 0.882353
149 FUC GAL GLA 0.457627 0.882353
150 GLA GAL FUC 0.457627 0.882353
151 FUC GLA GLA 0.457627 0.882353
152 G1P 0.456522 0.707317
153 GL1 0.456522 0.707317
154 XGP 0.456522 0.707317
155 M1P 0.456522 0.707317
156 ISX 0.454545 0.731707
157 GLA GAL NAG 0.453125 0.666667
158 MAN BMA NAG 0.453125 0.666667
159 SOR GLC GLC 0.451613 0.882353
160 FUC BGC GAL 0.45 0.882353
161 NAG BMA 0.45 0.625
162 MAN MAN MAN BMA MAN 0.447761 0.909091
163 MAN IFM 0.446429 0.697674
164 GLC IFM 0.446429 0.697674
165 WZ3 0.446154 0.833333
166 BMA MAN MAN MAN MAN 0.446154 0.909091
167 GLC GLC XYS 0.444444 0.882353
168 KHO 0.442308 0.805556
169 OPM MAN MAN 0.439394 0.731707
170 GLC 7LQ 0.438596 0.909091
171 BMA BMA GLA BMA BMA 0.4375 0.909091
172 GLO GLC GLC GLC 0.4375 0.882353
173 SOR GLC GLC GLC 0.4375 0.882353
174 6UZ 0.4375 0.769231
175 GAL NGT 0.435484 0.6
176 P3M 0.435484 0.697674
177 NGT GAL 0.435484 0.6
178 GLO GLC GLC 0.432836 0.857143
179 GTM BGC BGC 0.430769 0.789474
180 10M 0.430769 0.666667
181 4RS 0.423729 0.75
182 GLC BDF 0.423729 0.833333
183 56N 0.423077 0.909091
184 GLC GLC GLC BGC 0.421875 0.909091
185 RGG 0.42 0.90625
186 MAG FUC GAL 0.41791 0.625
187 GAL NAG MAN 0.41791 0.666667
188 NAG BMA MAN MAN MAN MAN MAN 0.416667 0.789474
189 XYT 0.416667 0.697674
190 BMA GLA 0.415094 0.909091
191 GAL GLC 0.415094 0.909091
192 LAK 0.415094 0.909091
193 MAN BMA 0.415094 0.909091
194 GLA BGC 0.415094 0.909091
195 GLA GLC 0.415094 0.909091
196 MAN MAN 0.415094 0.909091
197 BGC GLC 0.415094 0.909091
198 BMA MAN 0.415094 0.909091
199 GLA BMA 0.415094 0.909091
200 BGC GLA 0.415094 0.909091
201 GAL GAL 0.415094 0.909091
202 GLC BGC 0.415094 0.909091
203 GLC GLC 0.415094 0.909091
204 MLB 0.415094 0.909091
205 MA8 0.412698 0.612245
206 GAL BGC BGC XYS 0.411765 0.857143
207 DEG 0.411765 0.783784
208 GLA MMA ABE 0.409091 0.789474
209 GLA MAN ABE 0.409091 0.833333
210 GAL NAG GAL GLC 0.408451 0.666667
211 BGC GAL NAG GAL 0.408451 0.666667
212 MGL SGC BGC BGC 0.405797 0.789474
213 MGL SGC GLC GLC 0.405797 0.789474
214 BGC GLA GAL FUC 0.405797 0.882353
215 BGC BGC SGC MGL 0.405797 0.789474
216 CM5 0.405797 0.810811
217 2M8 0.403846 0.878788
218 GLC GLC GLC 0.4 0.909091
219 MAN MAN MAN 0.4 0.909091
220 GLC GLC GLC GLC GLC BGC 0.4 0.909091
221 MA4 0.4 0.810811
222 BMA MAN MAN 0.4 0.909091
223 GLC GLC GLC GLC BGC 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6EQ8; Ligand: BQZ; 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: 6eq8.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6EQ8; Ligand: BQZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6eq8.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6EQ8; Ligand: BQZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6eq8.bio4) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6EQ8; Ligand: BQZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6eq8.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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