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 552 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 426 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 322 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 (2D)
Ligand no: 1; Ligand: BQZ; Similar ligands found: 128
No: Ligand ECFP6 Tc MDL keys Tc
1 BQZ 1 1
2 GAL GLA 0.644444 0.909091
3 MBG GLA 0.622222 0.857143
4 BGC GLA GAL 0.622222 0.909091
5 MBG GAL 0.617021 0.857143
6 MGL GAL 0.583333 0.857143
7 BGC BGC BGC BGC BGC BGC BGC 0.58 0.909091
8 BGC BGC BGC 0.58 0.909091
9 BGC BGC BGC BGC BGC 0.58 0.909091
10 BGC BGC BGC BGC BGC BGC 0.58 0.909091
11 GLC BGC BGC BGC 0.58 0.909091
12 RR7 GLC 0.571429 0.857143
13 IPD MAN 0.568627 0.75
14 BGC GAL GLA 0.566038 0.909091
15 MYG 0.565217 0.789474
16 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.56 0.909091
17 GLC GLC GLC GLC BGC GLC GLC 0.56 0.909091
18 FUC GAL 0.56 0.909091
19 MAN BMA BMA BMA BMA BMA BMA 0.56 0.909091
20 RZM 0.55102 0.659091
21 MAN IPD MAN 0.54902 0.714286
22 GCU BGC 0.54717 0.882353
23 GLC EDO GLC 0.538462 0.857143
24 MAN MNM 0.528302 0.638298
25 BGC BGC BGC BGC BGC BGC BGC BGC 0.526316 0.909091
26 AHR FUB 0.522727 0.771429
27 5QP 0.519231 0.909091
28 FRU BMA 0.519231 0.763158
29 BGC XGP 0.518519 0.714286
30 BMA MAN MAN 0.517857 0.909091
31 MAN MAN MAN GLC 0.517241 0.909091
32 BGC OXZ 0.509434 0.638298
33 9MR 0.509434 0.714286
34 IFM BGC 0.509434 0.681818
35 GDQ GLC 0.509091 0.638298
36 GPM GLC 0.509091 0.697674
37 MMA MAN MAN 0.5 0.857143
38 GYP 0.5 0.878788
39 BGC 5VQ GAL GLA 0.5 0.810811
40 NOY BGC 0.5 0.638298
41 MAN BMA BMA 0.5 0.857143
42 MAN MAN 0.5 0.909091
43 G2F SHG BGC BGC 0.5 0.810811
44 MMA 0.5 0.878788
45 MGC GAL 0.5 0.638298
46 GAL SO4 GAL 0.5 0.6
47 NOJ GLC 0.5 0.666667
48 AMG 0.5 0.878788
49 MBG 0.5 0.878788
50 GLC DMJ 0.5 0.666667
51 CJX 0.490909 0.652174
52 ABL 0.490909 0.638298
53 DGO MAN 0.490566 0.882353
54 MAN G63 0.482143 0.625
55 GLC G6P 0.480769 0.714286
56 7D1 MAN 0.480769 0.857143
57 G2F BGC BGC BGC BGC BGC 0.474576 0.789474
58 GLC NBU GAL GLA 0.474576 0.769231
59 TVD GAL 0.473684 0.612245
60 NAG GAL 0.473684 0.666667
61 A2G GAL 0.473684 0.666667
62 FRU BGC BGC BGC 0.466667 0.789474
63 FRU GLC 0.462963 0.763158
64 GLC U8V 0.462963 0.833333
65 LSE 0.460317 0.625
66 G2I 0.459016 0.697674
67 UMQ 0.459016 0.714286
68 DMU 0.459016 0.714286
69 G3I 0.459016 0.697674
70 LMT 0.459016 0.714286
71 BGC OXZ BGC 0.459016 0.625
72 LMU 0.459016 0.714286
73 GAL FUC GAL 0.457627 0.882353
74 XGP 0.456522 0.707317
75 GL1 0.456522 0.707317
76 M1P 0.456522 0.707317
77 G1P 0.456522 0.707317
78 ISX 0.454545 0.731707
79 BGC BGC BGC BGC 0.453125 0.909091
80 NAG GAL GAL 0.453125 0.666667
81 SOR GLC GLC 0.451613 0.882353
82 MAN MAN BMA 0.45 0.857143
83 GLC BGC FUC GAL 0.45 0.882353
84 NAG BMA 0.45 0.625
85 BGC FUC GAL 0.45 0.882353
86 BGC GLC GLC 0.45 0.909091
87 GLC IFM 0.446429 0.697674
88 XYS GLC GLC 0.444444 0.882353
89 OPM MAN MAN 0.439394 0.731707
90 MAN MAN MAN 0.439394 0.882353
91 GLC 7LQ 0.438596 0.909091
92 BMA BMA BMA BMA GLA 0.4375 0.909091
93 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.4375 0.909091
94 GLC BGC BGC 0.4375 0.857143
95 6UZ 0.4375 0.769231
96 NGT GAL 0.435484 0.6
97 GLO GLC GLC 0.432836 0.857143
98 GLC GLC G6D ADH GLC GLC 0.430769 0.652174
99 GTM BGC BGC 0.430769 0.789474
100 10M 0.430769 0.666667
101 CK0 0.428571 0.652174
102 BDF GLC 0.423729 0.833333
103 56N 0.423077 0.909091
104 BGC GLC GLC GLC 0.421875 0.909091
105 GLC GLC GLC GLC GLC 0.421875 0.909091
106 GLO GLC GLC GLC 0.42029 0.857143
107 RGG 0.42 0.90625
108 MAN NAG GAL 0.41791 0.666667
109 NAG BMA MAN MAN MAN MAN MAN 0.416667 0.789474
110 MAN MAN M6P 0.415385 0.714286
111 BMA MAN MAN MAN MAN 0.414286 0.857143
112 MA8 0.412698 0.612245
113 GAL NAG GAL 0.411765 0.666667
114 DEG 0.411765 0.783784
115 BGC BGC XYS GAL 0.411765 0.857143
116 MMA GLA ABE 0.409091 0.789474
117 MAN GLA ABE 0.409091 0.833333
118 H1M MAN MAN 0.409091 0.789474
119 BGC GAL NAG GAL 0.408451 0.666667
120 GLC GLC GLC 0.40625 0.857143
121 MGL SGC BGC BGC 0.405797 0.789474
122 CM5 0.405797 0.810811
123 BGC GAL FUC GLA 0.405797 0.882353
124 2M8 0.403846 0.878788
125 BGC GLC GLC GLC GLC GLC 0.4 0.909091
126 MA4 0.4 0.810811
127 BGC GAL NGA GAL 0.4 0.666667
128 BGC GLC GLC GLC GLC 0.4 0.909091
Similar Ligands (3D)
Ligand no: 1; Ligand: BQZ; Similar ligands found: 37
No: Ligand Similarity coefficient
1 GLA GLA 0.9380
2 F9W 0.9130
3 GLC GLC 0.9079
4 GAT 0.9052
5 BGC GLC 0.9052
6 GLC GLA 0.9032
7 SGC GLC 0.9002
8 BGC BGC 0.9000
9 TW7 GLC 0.8994
10 BGC GAL 0.8958
11 MHD GAL 0.8950
12 GAA 0.8943
13 7D0 0.8913
14 BGC GLA 0.8911
15 GLA BEZ 0.8879
16 GLC BGC 0.8866
17 NBZ GLA 0.8844
18 GLC GAL 0.8840
19 XMM 0.8838
20 ADA ADA 0.8823
21 145 0.8782
22 MA1 GLC 0.8780
23 GTR ADA 0.8735
24 DSQ 0.8725
25 BMA GAL 0.8721
26 6EN 0.8711
27 TWJ SDY 0.8688
28 MAN BMA 0.8683
29 XYP GCU 0.8662
30 GAL PHB 0.8656
31 DS8 0.8604
32 147 0.8599
33 SHG BGC 0.8545
34 BMA BGC 0.8538
35 NXB 0.8532
36 BMA IFM 0.8531
37 SA0 0.8527
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 16 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 17 residues
No: Leader PDB Ligand Sequence Similarity
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