Receptor
PDB id Resolution Class Description Source Keywords
4RA1 1.75 Å NON-ENZYME: TRANSPORT PBP ACCA FROM A. TUMEFACIENS C58 IN COMPLEX WITH D-GLUCOSE-2 AGROBACTERIUM TUMEFACIENS PERIPLASMIC BINDING PROTEIN C CLUSTER TRANSPORT PROTEIN
Ref.: A PYRANOSE-2-PHOSPHATE MOTIF IS RESPONSIBLE FOR BOT ANTIBIOTIC IMPORT AND QUORUM-SENSING REGULATION IN AGROBACTERIUM TUMEFACIENS. PLOS PATHOG. V. 11 05071 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:606;
A:605;
A:607;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
BNX A:602;
 Valid;
 none;
 Kd = 0.43 uM
260.136 C6 H13 O9 P C([C@...
PEG A:604;
A:603;
 Invalid;
Invalid;
 none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
ALX A:601;
 Valid;
 none;
 Kd = 0.43 uM
260.136 C6 H13 O9 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RA1 1.75 Å NON-ENZYME: TRANSPORT PBP ACCA FROM A. TUMEFACIENS C58 IN COMPLEX WITH D-GLUCOSE-2 AGROBACTERIUM TUMEFACIENS PERIPLASMIC BINDING PROTEIN C CLUSTER TRANSPORT PROTEIN
Ref.: A PYRANOSE-2-PHOSPHATE MOTIF IS RESPONSIBLE FOR BOT ANTIBIOTIC IMPORT AND QUORUM-SENSING REGULATION IN AGROBACTERIUM TUMEFACIENS. PLOS PATHOG. V. 11 05071 2015
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 4ZEK - LAH C8 H17 O8 P CC(C)OP(=O....
2 4ZEI Kd = 1.33 uM LAO C5 H11 O8 P C1[C@@H]([....
3 4ZED - AGW C24 H35 O19 P c1ccc(cc1)....
4 4RA1 Kd = 0.43 uM BNX C6 H13 O9 P C([C@@H]1[....
5 6I7W Kd = 2 uM H6Z C9 H19 O11 P C[C@@H](C(....
6 4ZEB - ARA TT7 4GL n/a n/a
7 4ZEC - C84 C21 H34 N6 O16 P2 CC(C)[C@@H....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 4ZEK - LAH C8 H17 O8 P CC(C)OP(=O....
2 4ZEI Kd = 1.33 uM LAO C5 H11 O8 P C1[C@@H]([....
3 4ZED - AGW C24 H35 O19 P c1ccc(cc1)....
4 4RA1 Kd = 0.43 uM BNX C6 H13 O9 P C([C@@H]1[....
5 6I7W Kd = 2 uM H6Z C9 H19 O11 P C[C@@H](C(....
6 4ZEB - ARA TT7 4GL n/a n/a
7 4ZEC - C84 C21 H34 N6 O16 P2 CC(C)[C@@H....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 4ZEK - LAH C8 H17 O8 P CC(C)OP(=O....
2 4ZEI Kd = 1.33 uM LAO C5 H11 O8 P C1[C@@H]([....
3 4ZED - AGW C24 H35 O19 P c1ccc(cc1)....
4 4RA1 Kd = 0.43 uM BNX C6 H13 O9 P C([C@@H]1[....
5 6I7W Kd = 2 uM H6Z C9 H19 O11 P C[C@@H](C(....
6 4ZEB - ARA TT7 4GL n/a n/a
7 4ZEC - C84 C21 H34 N6 O16 P2 CC(C)[C@@H....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BNX; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 BNX 1 1
2 ALX 1 1
3 H6Q 0.568627 0.97561
4 H6Z 0.568627 0.97561
5 2GS 0.512195 0.674419
6 R1P 0.465116 0.904762
7 GL1 0.434783 1
8 M1P 0.434783 1
9 G1P 0.434783 1
10 XGP 0.434783 1
11 GFP 0.408163 0.909091
12 GP1 0.408163 0.833333
13 2IP 0.405405 0.707317
14 AHR 0.405405 0.619048
15 32O 0.405405 0.619048
16 RIB 0.405405 0.619048
17 BDR 0.405405 0.619048
18 Z6J 0.405405 0.619048
19 FUB 0.405405 0.619048
20 MQG 0.4 0.730769
21 HSX 0.4 0.880952
22 ABF 0.4 0.880952
23 RP5 0.4 0.880952
Ligand no: 2; Ligand: ALX; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 BNX 1 1
2 ALX 1 1
3 H6Q 0.568627 0.97561
4 H6Z 0.568627 0.97561
5 2GS 0.512195 0.674419
6 R1P 0.465116 0.904762
7 GL1 0.434783 1
8 M1P 0.434783 1
9 G1P 0.434783 1
10 XGP 0.434783 1
11 GFP 0.408163 0.909091
12 GP1 0.408163 0.833333
13 2IP 0.405405 0.707317
14 AHR 0.405405 0.619048
15 32O 0.405405 0.619048
16 RIB 0.405405 0.619048
17 BDR 0.405405 0.619048
18 Z6J 0.405405 0.619048
19 FUB 0.405405 0.619048
20 MQG 0.4 0.730769
21 HSX 0.4 0.880952
22 ABF 0.4 0.880952
23 RP5 0.4 0.880952
Similar Ligands (3D)
Ligand no: 1; Ligand: BNX; Similar ligands found: 243
No: Ligand Similarity coefficient
1 NAG 0.9774
2 LTM 0.9624
3 GDL 0.9585
4 NDG 0.9548
5 MAG 0.9519
6 FDR 0.9423
7 BEU 0.9422
8 LOG 0.9420
9 PH2 0.9408
10 NOK 0.9389
11 NGA 0.9380
12 SNG 0.9377
13 HHR 0.9365
14 5NS 0.9360
15 DNA 0.9347
16 GJP 0.9341
17 8MO 0.9340
18 9H2 0.9339
19 EUE 0.9316
20 HHS 0.9291
21 S0E 0.9277
22 H5B 0.9272
23 Y0V 0.9258
24 68A 0.9235
25 8NB 0.9217
26 4RU 0.9196
27 ZEC 0.9191
28 E1K 0.9182
29 KYA 0.9163
30 KGK 0.9160
31 LP8 0.9148
32 6KT 0.9127
33 KJ5 0.9122
34 L1Q 0.9121
35 BGN 0.9119
36 PRF 0.9113
37 4KL 0.9112
38 M78 0.9109
39 QMS 0.9092
40 2KA 0.9092
41 PLP 0.9080
42 MNS 0.9073
43 L7T 0.9073
44 THA 0.9072
45 IPD 0.9070
46 TNX 0.9069
47 OQC 0.9063
48 BHQ 0.9057
49 BM3 0.9055
50 2CZ 0.9053
51 A2G 0.9045
52 LIP 0.9044
53 2K8 0.9043
54 JTH 0.9039
55 EVF 0.9033
56 MAJ 0.9027
57 LZ2 0.9026
58 MUR 0.9017
59 2O6 0.9016
60 RH1 0.9014
61 BBK 0.9014
62 54Z 0.9012
63 0J4 0.9005
64 S0G 0.9000
65 HQ6 0.8998
66 QQQ 0.8997
67 2L3 0.8994
68 21D 0.8991
69 5GV 0.8990
70 GO2 0.8974
71 GF4 0.8972
72 27B 0.8969
73 EXD 0.8966
74 KMY 0.8966
75 IFG 0.8962
76 5RO 0.8954
77 SG2 0.8953
78 PMP 0.8952
79 9KZ 0.8951
80 UNJ 0.8947
81 N2M 0.8945
82 0FN 0.8945
83 APS 0.8938
84 BA5 0.8937
85 HBI 0.8937
86 9R5 0.8936
87 GNM 0.8932
88 I4D 0.8931
89 2F8 0.8920
90 SIZ 0.8918
91 86L 0.8916
92 1F1 0.8915
93 15N 0.8913
94 HNT 0.8912
95 P9E 0.8912
96 8WO 0.8910
97 ARP 0.8904
98 7B3 0.8899
99 IAC 0.8899
100 YX1 0.8898
101 STZ 0.8898
102 TWO 0.8895
103 AA 0.8893
104 LAO 0.8891
105 5GT 0.8889
106 6HP 0.8883
107 9ZE 0.8876
108 3A9 0.8875
109 K3Q 0.8867
110 AU8 0.8856
111 NBG 0.8852
112 1BW 0.8849
113 BIO 0.8843
114 N0Z 0.8841
115 A7H 0.8835
116 IOS 0.8834
117 0JD 0.8831
118 F34 0.8829
119 54X 0.8828
120 H4B 0.8824
121 CEG 0.8823
122 1HN 0.8822
123 M5H 0.8821
124 ST2 0.8819
125 SKF 0.8817
126 B56 0.8812
127 3Y7 0.8812
128 9FE 0.8811
129 0FK 0.8810
130 H2B 0.8807
131 X04 0.8807
132 ST3 0.8806
133 EE8 0.8804
134 DJN 0.8802
135 F5C 0.8802
136 57O 0.8802
137 FWD 0.8796
138 PZP 0.8786
139 MP5 0.8784
140 4NP 0.8784
141 N1E 0.8784
142 IOP 0.8783
143 505 0.8782
144 7AP 0.8781
145 PXP 0.8780
146 ZYR 0.8779
147 3R4 0.8777
148 ANF 0.8776
149 S8A 0.8775
150 ZZZ 0.8771
151 3VX 0.8770
152 2QC 0.8759
153 3TV 0.8759
154 657 0.8759
155 3N1 0.8756
156 K82 0.8754
157 YO5 0.8753
158 GC2 0.8753
159 BHS 0.8751
160 0J5 0.8750
161 DRG 0.8749
162 CWD 0.8748
163 92O 0.8747
164 ZPF 0.8744
165 N91 0.8744
166 89J 0.8743
167 B52 0.8739
168 790 0.8737
169 VPU 0.8737
170 G6P 0.8736
171 BG6 0.8736
172 4JC 0.8736
173 4NS 0.8735
174 MD6 0.8730
175 KF5 0.8729
176 7MX 0.8727
177 88L 0.8722
178 CFA 0.8719
179 GCU 0.8715
180 HA5 0.8714
181 46M 0.8714
182 4AB 0.8712
183 3XR 0.8706
184 1FD 0.8703
185 DDU 0.8703
186 ST1 0.8701
187 54E 0.8699
188 5NE 0.8693
189 3J8 0.8692
190 JF2 0.8692
191 HHT 0.8689
192 CC5 0.8688
193 3D1 0.8686
194 BGC 0.8684
195 8HC 0.8680
196 4R1 0.8679
197 9BF 0.8676
198 DHY 0.8675
199 HBO 0.8673
200 TSR 0.8672
201 IBM 0.8672
202 AP4 0.8672
203 NEU 0.8666
204 CTE 0.8666
205 CP7 0.8665
206 9GP 0.8658
207 3C4 0.8657
208 MCY 0.8652
209 537 0.8648
210 B86 0.8647
211 P0P 0.8645
212 JXK 0.8644
213 PNP 0.8640
214 CR1 0.8638
215 4SX 0.8637
216 AES 0.8635
217 BQ2 0.8631
218 E1T 0.8631
219 F4K 0.8630
220 80G 0.8629
221 NFM 0.8626
222 SY4 0.8625
223 K68 0.8625
224 5TY 0.8624
225 MPU 0.8621
226 SYE 0.8617
227 ZYX 0.8617
228 JXW 0.8611
229 X0T 0.8610
230 L1O 0.8608
231 4JE 0.8608
232 FTV 0.8602
233 5WU 0.8599
234 E7R 0.8593
235 JYT 0.8593
236 KLK 0.8593
237 L46 0.8570
238 GSY 0.8569
239 PYU 0.8563
240 F52 0.8557
241 E3D 0.8550
242 3W8 0.8532
243 5MD 0.8523
Ligand no: 2; Ligand: ALX; Similar ligands found: 117
No: Ligand Similarity coefficient
1 NDG 0.9739
2 NAG 0.9666
3 GDL 0.9545
4 LIP 0.9519
5 2F8 0.9447
6 LOG 0.9414
7 NOK 0.9363
8 A2G 0.9307
9 NGA 0.9233
10 BM3 0.9079
11 ZPF 0.9068
12 GLP 0.9050
13 BGN 0.9046
14 SNG 0.9034
15 8NB 0.9023
16 DJN 0.9013
17 MAG 0.8999
18 BBK 0.8996
19 G6P 0.8993
20 86L 0.8988
21 1FD 0.8986
22 54Z 0.8984
23 4NS 0.8980
24 PMP 0.8952
25 657 0.8945
26 GF4 0.8942
27 APS 0.8937
28 1BW 0.8932
29 BG6 0.8928
30 428 0.8911
31 8U3 0.8909
32 2CZ 0.8904
33 S8A 0.8901
34 QMS 0.8900
35 X04 0.8898
36 JTH 0.8892
37 ARP 0.8889
38 MP5 0.8883
39 4R1 0.8861
40 K82 0.8858
41 IPD 0.8855
42 PLP 0.8849
43 88L 0.8845
44 PZP 0.8834
45 4NP 0.8820
46 2K8 0.8817
47 MAJ 0.8812
48 3VX 0.8811
49 PNP 0.8800
50 EXD 0.8799
51 H4B 0.8791
52 PXP 0.8790
53 OQC 0.8787
54 TMG 0.8786
55 2KA 0.8785
56 UA5 0.8771
57 SYE 0.8769
58 F5C 0.8762
59 5GT 0.8759
60 9H2 0.8755
61 A5P 0.8754
62 EVF 0.8749
63 S0G 0.8746
64 505 0.8740
65 SKF 0.8736
66 CTE 0.8733
67 I4D 0.8732
68 GZV 0.8728
69 3C4 0.8724
70 ZON 0.8713
71 K3Q 0.8711
72 0JD 0.8710
73 WS7 0.8709
74 YTX 0.8696
75 GF1 0.8695
76 IOS 0.8690
77 3XR 0.8684
78 IAC 0.8678
79 5GV 0.8677
80 M6P 0.8670
81 27B 0.8666
82 ST2 0.8665
83 HNT 0.8662
84 CFA 0.8655
85 9BF 0.8654
86 EYV 0.8652
87 MD6 0.8647
88 HBI 0.8645
89 5OO 0.8645
90 HHT 0.8640
91 8WO 0.8639
92 3Y7 0.8632
93 MS0 0.8628
94 RH1 0.8625
95 EUH 0.8624
96 KF5 0.8621
97 MUR 0.8613
98 2O8 0.8609
99 L1Q 0.8602
100 DHY 0.8601
101 P0P 0.8597
102 6HP 0.8594
103 I2E 0.8580
104 S24 0.8577
105 STT 0.8575
106 0J4 0.8573
107 0J5 0.8562
108 3N1 0.8561
109 BY5 0.8558
110 TSR 0.8552
111 KJ5 0.8547
112 DTE 0.8540
113 TWO 0.8535
114 RES 0.8521
115 PQK 0.8520
116 LAO 0.8519
117 M3Q 0.8517
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RA1; Ligand: BNX; 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: 4ra1.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RA1; Ligand: BNX; 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: 4ra1.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4RA1; Ligand: ALX; 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: 4ra1.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4RA1; Ligand: ALX; 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: 4ra1.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4RA1; Ligand: BNX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4ra1.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4RA1; Ligand: ALX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4ra1.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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