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 544 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 TTV GLC ZCD GLA n/a n/a
4 6EPZ Kd = 0.76 uM GLC GLA n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 420 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 TTV GLC ZCD GLA n/a n/a
4 6EPZ Kd = 0.76 uM GLC GLA n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 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 TTV GLC ZCD GLA n/a n/a
4 6EPZ Kd = 0.76 uM GLC GLA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BQZ; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 BQZ 1 1
2 TRE 0.675676 0.909091
3 GLC BGC 0.644444 0.909091
4 MAN GLC 0.644444 0.909091
5 GLC GLC 0.644444 0.909091
6 GLA GLA 0.644444 0.909091
7 GLA GAL 0.644444 0.909091
8 M3M 0.644444 0.909091
9 NGR 0.644444 0.909091
10 LB2 0.644444 0.909091
11 BMA MAN 0.622222 0.909091
12 BGC GLC 0.622222 0.909091
13 LAT GLA 0.622222 0.909091
14 GLA MBG 0.622222 0.857143
15 2M4 0.622222 0.909091
16 MDM 0.617021 0.857143
17 M13 0.617021 0.857143
18 GAL MBG 0.617021 0.857143
19 MAN MMA 0.617021 0.857143
20 B2G 0.608696 0.909091
21 N9S 0.608696 0.909091
22 BGC GAL 0.608696 0.909091
23 CBK 0.608696 0.909091
24 LAT 0.608696 0.909091
25 MAB 0.608696 0.909091
26 LBT 0.608696 0.909091
27 MAL 0.608696 0.909091
28 BGC BMA 0.608696 0.909091
29 CBI 0.608696 0.909091
30 BMA GAL 0.608696 0.909091
31 GAL BGC 0.608696 0.909091
32 GLC GAL 0.608696 0.909091
33 BMA BMA 0.608696 0.909091
34 MMA MAN 0.583333 0.857143
35 DR5 0.583333 0.857143
36 GLC GLC GLC GLC 0.58 0.909091
37 BGC BGC BGC BGC BGC BGC 0.58 0.909091
38 GLC BGC BGC BGC BGC BGC BGC 0.58 0.909091
39 GLC GLC GLC 0.58 0.909091
40 BGC BGC BGC GLC BGC BGC 0.58 0.909091
41 GLC GLC BGC 0.58 0.909091
42 DOM 0.571429 0.857143
43 GLA GAL GAL 0.566038 0.909091
44 MYG 0.565217 0.789474
45 DXI 0.56 0.909091
46 CTT 0.56 0.909091
47 BMA BMA BMA 0.56 0.909091
48 BGC BGC BGC BGC 0.56 0.909091
49 B4G 0.56 0.909091
50 GLC BGC BGC BGC BGC BGC 0.56 0.909091
51 GLC GAL GAL 0.56 0.909091
52 GLC BGC BGC BGC BGC 0.56 0.909091
53 CT3 0.56 0.909091
54 MLR 0.56 0.909091
55 MAN MAN BMA BMA BMA BMA 0.56 0.909091
56 GLC BGC GLC 0.56 0.909091
57 BGC GLC GLC GLC GLC GLC GLC 0.56 0.909091
58 BMA BMA BMA BMA BMA BMA 0.56 0.909091
59 BMA BMA BMA BMA BMA 0.56 0.909091
60 BGC BGC BGC 0.56 0.909091
61 CE6 0.56 0.909091
62 CE5 0.56 0.909091
63 GLC BGC BGC BGC 0.56 0.909091
64 BGC GLC GLC GLC GLC 0.56 0.909091
65 BGC GLC GLC GLC 0.56 0.909091
66 GLA GAL GLC 0.56 0.909091
67 GLC BGC BGC 0.56 0.909091
68 GAL GAL GAL 0.56 0.909091
69 MT7 0.56 0.909091
70 CEY 0.56 0.909091
71 GLA GAL BGC 0.56 0.909091
72 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.56 0.909091
73 CTR 0.56 0.909091
74 CEX 0.56 0.909091
75 MAN BMA BMA BMA BMA 0.56 0.909091
76 BGC BGC GLC 0.56 0.909091
77 BMA MAN BMA 0.56 0.909091
78 BGC BGC BGC GLC 0.56 0.909091
79 CE8 0.56 0.909091
80 BGC GLC GLC 0.56 0.909091
81 MAN BMA BMA 0.56 0.909091
82 GAL FUC 0.56 0.909091
83 MTT 0.56 0.909091
84 GLC GLC GLC GLC GLC 0.56 0.909091
85 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.56 0.909091
86 MAN BMA BMA BMA BMA BMA 0.56 0.909091
87 RZM 0.55102 0.659091
88 GLA EGA 0.54902 0.857143
89 CGC 0.54717 0.909091
90 BGC BGC 0.54 0.882353
91 MAN MAN BMA 0.538462 0.909091
92 MAL EDO 0.538462 0.857143
93 BMA BMA MAN 0.538462 0.909091
94 U63 0.529412 0.810811
95 BGC BGC BGC BGC BGC 0.528302 0.909091
96 BGC BGC BGC BGC BGC BGC BGC 0.528302 0.909091
97 MAN MNM 0.528302 0.638298
98 BMA MAN MAN MAN 0.527273 0.909091
99 BGC BGC BGC BGC BGC BGC BGC BGC 0.526316 0.909091
100 W9T 0.519231 0.763158
101 BMA FRU 0.519231 0.763158
102 FRU GAL 0.519231 0.763158
103 5QP 0.519231 0.909091
104 MVP 0.518519 0.666667
105 MAN BMA MAN 0.517857 0.909091
106 MAN MAN MAN 0.517857 0.909091
107 MAN MAN MAN GLC 0.517241 0.909091
108 BMA IFM 0.509434 0.681818
109 9MR 0.509434 0.714286
110 IFM BMA 0.509434 0.681818
111 BGC OXZ 0.509434 0.638298
112 IFM BGC 0.509434 0.681818
113 GDQ GLC 0.509091 0.638298
114 NOJ GLC 0.5 0.666667
115 AMG 0.5 0.878788
116 GYP 0.5 0.878788
117 MMA 0.5 0.878788
118 GLC DMJ 0.5 0.666667
119 FMO 0.5 0.789474
120 GLA GAL BGC 5VQ 0.5 0.810811
121 GAL GAL SO4 0.5 0.6
122 NOY BGC 0.5 0.638298
123 MBG 0.5 0.878788
124 MAN MMA MAN 0.5 0.857143
125 GAL MGC 0.5 0.638298
126 ABL 0.490909 0.638298
127 MAN DGO 0.490566 0.882353
128 T6P 0.490196 0.697674
129 MAN G63 0.482143 0.625
130 MAN 7D1 0.480769 0.857143
131 MAN MAN MAN MAN 0.47541 0.909091
132 MAN MAN BMA MAN 0.47541 0.909091
133 G2F BGC BGC BGC BGC BGC 0.474576 0.789474
134 GLA GAL GLC NBU 0.474576 0.769231
135 NLC 0.473684 0.666667
136 GAL NDG 0.473684 0.666667
137 GAL NAG 0.473684 0.666667
138 8VZ 0.473684 0.612245
139 GAL NGA 0.473684 0.666667
140 NAG GAL 0.473684 0.666667
141 GAL A2G 0.473684 0.666667
142 M5S 0.467742 0.909091
143 MAN BMA MAN MAN MAN 0.467742 0.909091
144 BGC BGC BGC FRU 0.466667 0.789474
145 BMA BMA MAN GLA GLA 0.466667 0.909091
146 TUR 0.462963 0.763158
147 GLC FRU 0.462963 0.763158
148 BTU 0.462963 0.763158
149 LSE 0.460317 0.625
150 G2I 0.459016 0.697674
151 LMT 0.459016 0.714286
152 LMU 0.459016 0.714286
153 DMU 0.459016 0.714286
154 GLC GLC XYP 0.459016 0.909091
155 OXZ BGC BGC 0.459016 0.625
156 G3I 0.459016 0.697674
157 UMQ 0.459016 0.714286
158 GLA GAL FUC 0.457627 0.882353
159 FUC GAL GLA 0.457627 0.882353
160 GAL GAL FUC 0.457627 0.882353
161 GLA GLA FUC 0.457627 0.882353
162 FUC GLA GLA 0.457627 0.882353
163 G1P 0.456522 0.707317
164 M1P 0.456522 0.707317
165 XGP 0.456522 0.707317
166 GL1 0.456522 0.707317
167 ISX 0.454545 0.731707
168 MAN BMA NAG 0.453125 0.666667
169 GLA GAL NAG 0.453125 0.666667
170 SOR GLC GLC 0.451613 0.882353
171 FUC GLC BGC GAL 0.45 0.882353
172 FUC BGC GAL 0.45 0.882353
173 NAG BMA 0.45 0.625
174 A2G GAL 0.45 0.625
175 MAN MAN MAN BMA MAN 0.447761 0.909091
176 GLC IFM 0.446429 0.697674
177 MAN IFM 0.446429 0.697674
178 BMA MAN MAN MAN MAN 0.446154 0.909091
179 WZ3 0.446154 0.833333
180 GLC GLC XYS 0.444444 0.882353
181 KHO 0.442308 0.805556
182 OPM MAN MAN 0.439394 0.731707
183 GLC 7LQ 0.438596 0.909091
184 BMA BMA BMA GLA BMA 0.4375 0.909091
185 SOR GLC GLC GLC 0.4375 0.882353
186 6UZ 0.4375 0.769231
187 GLO GLC GLC GLC 0.4375 0.882353
188 BMA BMA GLA BMA BMA 0.4375 0.909091
189 P3M 0.435484 0.697674
190 NGT GAL 0.435484 0.6
191 GAL NGT 0.435484 0.6
192 GLO GLC GLC 0.432836 0.857143
193 10M 0.430769 0.666667
194 GTM BGC BGC 0.430769 0.789474
195 GLC BDF 0.423729 0.833333
196 4RS 0.423729 0.75
197 56N 0.423077 0.909091
198 GLC GLC GLC BGC 0.421875 0.909091
199 RGG 0.42 0.90625
200 GAL NAG MAN 0.41791 0.666667
201 MAG FUC GAL 0.41791 0.625
202 XYT 0.416667 0.697674
203 GLA GLC 0.415094 0.909091
204 BGC GLA 0.415094 0.909091
205 MAN MAN 0.415094 0.909091
206 MLB 0.415094 0.909091
207 GLA BGC 0.415094 0.909091
208 GAL GLC 0.415094 0.909091
209 LAK 0.415094 0.909091
210 GAL GAL 0.415094 0.909091
211 BMA GLA 0.415094 0.909091
212 GLA BMA 0.415094 0.909091
213 MAN BMA 0.415094 0.909091
214 MA8 0.412698 0.612245
215 DEG 0.411765 0.783784
216 GAL BGC BGC XYS 0.411765 0.857143
217 GLA MAN ABE 0.409091 0.833333
218 GLA MMA ABE 0.409091 0.789474
219 BGC GAL NAG GAL 0.408451 0.666667
220 GAL NAG GAL GLC 0.408451 0.666667
221 MGL SGC BGC BGC 0.405797 0.789474
222 CM5 0.405797 0.810811
223 BGC GLA GAL FUC 0.405797 0.882353
224 MGL SGC GLC GLC 0.405797 0.789474
225 BGC BGC SGC MGL 0.405797 0.789474
226 2M8 0.403846 0.878788
227 GLC GLC GLC GLC GLC BGC 0.4 0.909091
228 GLC GLC GLC GLC BGC 0.4 0.909091
229 BMA MAN MAN 0.4 0.909091
230 MA4 0.4 0.810811
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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