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Receptor
PDB id Resolution Class Description Source Keywords
5W71 2.1 Å EC: 2.6.1.- X-RAY STRUCTURE OF BTRR FROM BACILLUS CIRCULANS IN THE PRESE 2-DOS EXTERNAL ALDIMINE BACILLUS CIRCULANS BUTIROSIN AMINOTRANSFERASE AMINOGLYCOSIDE AMINOCYCLITOL ANTIBIOTIC TRANSFERASE
Ref.: THE STRUCTURE OF RBMB FROM STREPTOMYCES RIBOSIDIFIC AMINOTRANSFERASE INVOLVED IN THE BIOSYNTHESIS OF RIBOSTAMYCIN. PROTEIN SCI. V. 26 1886 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL B:502;
Invalid;
none;
submit data
35.453 Cl [Cl-]
PLP A:501;
Valid;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
9YM B:501;
Valid;
none;
submit data
393.329 C14 H24 N3 O8 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W71 2.1 Å EC: 2.6.1.- X-RAY STRUCTURE OF BTRR FROM BACILLUS CIRCULANS IN THE PRESE 2-DOS EXTERNAL ALDIMINE BACILLUS CIRCULANS BUTIROSIN AMINOTRANSFERASE AMINOGLYCOSIDE AMINOCYCLITOL ANTIBIOTIC TRANSFERASE
Ref.: THE STRUCTURE OF RBMB FROM STREPTOMYCES RIBOSIDIFIC AMINOTRANSFERASE INVOLVED IN THE BIOSYNTHESIS OF RIBOSTAMYCIN. PROTEIN SCI. V. 26 1886 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2C81 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 5W71 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2C81 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 5W71 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 2C81 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
2 5W71 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 5W70 - 9YM C14 H24 N3 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 F0G 0.564516 0.865385
12 MPM 0.564516 0.814815
13 FEV 0.555556 0.803571
14 KOU 0.555556 0.836364
15 HCP 0.546875 0.77193
16 EVM 0.546875 0.821429
17 6DF 0.545455 0.811321
18 PXL 0.541667 0.659574
19 Z98 0.537313 0.75
20 PXP 0.537037 0.862745
21 PMP 0.527273 0.767857
22 P0P 0.527273 0.916667
23 PL6 0.522388 0.818182
24 GT1 0.517857 0.830189
25 PFM 0.514706 0.803571
26 FEJ 0.514706 0.851852
27 LLP 0.5 0.737705
28 P70 0.5 0.833333
29 PUS 0.479452 0.707692
30 PL5 0.479452 0.775862
31 MPL 0.473684 0.836364
32 PLG 0.46875 0.75
33 IN5 0.46875 0.758621
34 P89 0.466667 0.714286
35 PLP PUT 0.463768 0.672131
36 EQJ 0.460526 0.725806
37 5DK 0.460526 0.725806
38 O1G 0.454545 0.75
39 PLT 0.439024 0.762712
40 X04 0.431034 0.851852
41 PDD 0.426471 0.762712
42 PP3 0.426471 0.762712
43 PDA 0.426471 0.762712
44 P1T 0.426471 0.714286
45 33P 0.42029 0.745763
46 IK2 0.42029 0.714286
47 TLP 0.414286 0.793103
48 2BK 0.414286 0.793103
49 PLS 0.414286 0.779661
50 2BO 0.414286 0.793103
51 5PA 0.414286 0.714286
52 PMH 0.414286 0.619718
53 9TD 0.413793 0.671642
54 PLP 999 0.410959 0.796296
55 PPD 0.408451 0.75
56 C6P 0.408451 0.75
57 QLP 0.405405 0.681818
58 MP5 0.403509 0.666667
59 PLA 0.402778 0.703125
60 PY5 0.402778 0.703125
61 HEY 0.4 0.703125
62 PLP PHE 0.4 0.732143
Ligand no: 2; Ligand: 9YM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 9YM 1 1
2 DCS 0.535714 0.797297
3 5PA 0.512195 0.835821
4 PLG 0.506329 0.818182
5 IN5 0.506329 0.828125
6 PDD 0.506173 0.80303
7 PDA 0.506173 0.80303
8 PP3 0.506173 0.80303
9 33P 0.5 0.787879
10 PLA 0.5 0.797101
11 PMP 0.493151 0.868852
12 P1T 0.487805 0.808824
13 PMG 0.482759 0.774648
14 IK2 0.481928 0.808824
15 PXP 0.479452 0.803279
16 TLP 0.47619 0.830769
17 PMH 0.47619 0.780822
18 2BK 0.47619 0.830769
19 2BO 0.47619 0.830769
20 PLS 0.47619 0.875
21 EA5 0.47191 0.811594
22 7TS 0.471264 0.74026
23 ILP 0.471264 0.779412
24 PPD 0.470588 0.846154
25 C6P 0.470588 0.846154
26 GT1 0.466667 0.723077
27 QLP 0.465909 0.8
28 PL2 0.465909 0.797101
29 PY5 0.465116 0.797101
30 DOW 0.462264 0.924242
31 7B9 0.457447 0.802817
32 RW2 0.456522 0.785714
33 ORX 0.455556 0.835821
34 PSZ 0.455556 0.736111
35 CBA 0.454545 0.820895
36 7XF 0.454545 0.820895
37 PGU 0.454545 0.820895
38 PDG 0.454545 0.820895
39 PL8 0.451613 0.77027
40 PE1 0.450549 0.835821
41 LPI 0.449438 0.763889
42 HEY 0.444444 0.771429
43 PY6 0.444444 0.774648
44 76U 0.444444 0.782609
45 PL4 0.44086 0.835821
46 N5F 0.43956 0.808824
47 3LM 0.43956 0.726027
48 PXG 0.425532 0.818182
49 KAM 0.416667 0.757143
50 AQ3 0.414141 0.850746
51 2QR 0.409449 0.75
52 LCS 0.402174 0.736842
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W71; Ligand: PLP; Similar sites found with APoc: 154
This union binding pocket(no: 1) in the query (biounit: 5w71.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1TOI HCI 1.0101
2 2TPL HPP 1.13636
3 1CL2 PPG 1.26582
4 1M1B SPV 1.35593
5 1MLY ACZ PLP 1.3986
6 4UHO PLP 1.59091
7 6CZY PMP 1.65746
8 1DFO PLG 1.67866
9 2FYF PLP 1.75879
10 4BA5 PXG 1.81818
11 5G4J EXT 1.81818
12 3A8U PLP 1.81818
13 5W8X UDP 1.83246
14 3M0J OAF 1.9544
15 1OXO IK2 1.99501
16 5TXR PLP 2.04545
17 3VP6 HLD 2.04545
18 5LTJ BEF 2.04545
19 6F97 FAD 2.04545
20 4YIW NCD 2.04545
21 1GEX PLP HSA 2.24719
22 3EI9 PL6 2.27273
23 1U26 IHS 2.37389
24 1LC8 33P 2.47253
25 1PMO PLR 2.5
26 6H3O FAD 2.5
27 5HSA FAS 2.5
28 2Z9V PXM 2.55102
29 1AJS PLA 2.6699
30 4LNL PLG 2.7027
31 4LNL 2BK 2.7027
32 4LNL 2BO 2.7027
33 5GVL GI8 2.72727
34 5GVL PLG 2.72727
35 3GDN FAD 2.72727
36 4AZJ SEP PLP 2.77778
37 3WGC PLG 2.93255
38 4DOE CBK 2.94737
39 4ZM4 PLP 2.95455
40 6ECG PM9 2.95455
41 4AOA IK2 2.95455
42 4JE5 PLP 2.95455
43 4JE5 PMP 2.95455
44 4ZM4 P3B 2.95455
45 4B98 PXG 2.95455
46 2R2N PMP 3.05882
47 2R2N KYN 3.05882
48 4ZSY RW2 3.18182
49 3BS8 PMP 3.19635
50 1M7Y PPG 3.21839
51 1K4M CIT 3.28639
52 2CJH AKG 3.34076
53 1WYV PLP AOA 3.40909
54 6FYQ PLP 3.40909
55 6C92 EQJ 3.45745
56 6C8T EQJ 3.45745
57 6C9B EGV 3.45745
58 4RKC PMP 3.51759
59 3BWN PMP 3.58056
60 3BWN PMP PHE 3.58056
61 5BSH PRO 3.61011
62 2HHP FLC 3.63636
63 4ADC PLP 3.69458
64 4WXG 2BO 3.73832
65 3CQ5 PMP 3.79404
66 4UOX PLP 3.86364
67 4UOX PUT 3.86364
68 4UOX PLP PUT 3.86364
69 3ZRR PXG 3.90625
70 2X5F PLP 3.95349
71 1E5F PLP 3.9604
72 1WB4 SXX 4.0404
73 6C3C EJ1 4.31818
74 1DL5 SAH 4.4164
75 5W19 9TD 4.54545
76 1JS3 PLP 142 4.54545
77 3BGD PM6 4.61538
78 1W6F ISZ 4.67626
79 2HOX P1T 4.68384
80 3FQ8 PMP 4.77273
81 4E1O PLP PVH 5
82 4HVK PMP 5.2356
83 5TDC NMM ILE PHE SER 5.26316
84 2JBH 5GP 5.33333
85 4E3Q PMP 5.45455
86 5YKT PMP 5.45455
87 1M32 PLP 5.46448
88 1XXR MAN 5.59006
89 2XBN PMP 5.62061
90 6DND PLP 5.68182
91 5KGS 6SR 5.68182
92 6CBO DOW 5.69476
93 5IWQ PLP 5.76037
94 6CD1 PLG 6.13636
95 6CD1 PLS 6.13636
96 5DDW 5B6 6.13636
97 1UU1 PMP HSA 6.56716
98 2OAT PFM 6.83371
99 1SFF IK2 7.04225
100 1ZC9 PMP 7.04545
101 1DJ9 KAM 7.29167
102 5H3A UMP 7.42049
103 2WK9 PLG 7.45501
104 2WK9 PLP 7.45501
105 3PDB PMP 7.98005
106 3PD6 PMP 7.98005
107 5AHO TLA 8.03571
108 6CBN OZY 8.6758
109 1VJO PLP 8.90585
110 4WGF HX2 9.26829
111 5LUN OGA 9.375
112 5LUN ARG 9.375
113 1FC4 AKB PLP 9.47631
114 5X30 4LM 10.3015
115 5X30 7XF 10.3015
116 5X2Z 3LM 10.3015
117 4IY7 KOU 10.5793
118 4IY7 0JO 10.5793
119 4IYO 0JO 10.5793
120 4M2K PLP 10.5911
121 5TQZ GLC 10.6667
122 5VEQ PMP 10.7056
123 5WYF ILP 10.9091
124 2R5C C6P 11.4219
125 2R5E QLP 11.4219
126 1LW4 PLP 11.5274
127 1LW4 TLP 11.5274
128 1XI9 PLP 12.3153
129 2ZYJ PGU 12.8463
130 4P83 U5P 13.7363
131 2X5D PLP 13.835
132 4RJD TFP 15.1515
133 1GCK ASP PLP 16.6234
134 2ZC0 PMP 16.9533
135 5M3Z PY6 17.3367
136 5M3Z NLE 17.3367
137 5M3Z PLP 17.3367
138 1ELU PDA 19.7436
139 1ELU CSS 19.7436
140 6EWR PMP 25.0585
141 2FNU PMP UD1 30.4
142 2PO3 T4K 32.3113
143 5K8B PDG 34.4913
144 1O69 X04 36.2944
145 1MDZ PLP 38.4224
146 1MDZ DCS 38.4224
147 3NUB UD0 38.4401
148 4K2M O1G 39.5455
149 3B8X G4M 40.2564
150 4ZAH T5K 40.6566
151 3FRK TQP 41.2869
152 2OGA PGU 42.3559
153 5U23 TQP 43.9791
154 3DR4 G4M 48.0818
Pocket No.: 2; Query (leader) PDB : 5W71; Ligand: 9YM; Similar sites found with APoc: 132
This union binding pocket(no: 2) in the query (biounit: 5w71.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 1TOI HCI 1.0101
2 1CL2 PPG 1.26582
3 1MLY ACZ PLP 1.3986
4 4UHO PLP 1.59091
5 6CZY PMP 1.65746
6 1DFO PLG 1.67866
7 2FYF PLP 1.75879
8 3A8U PLP 1.81818
9 4BA5 PXG 1.81818
10 5G4J EXT 1.81818
11 5W8X UDP 1.83246
12 1OXO IK2 1.99501
13 5TXR PLP 2.04545
14 4YIW NCD 2.04545
15 5LTJ BEF 2.04545
16 3EI9 PL6 2.27273
17 1U26 IHS 2.37389
18 1LC8 33P 2.47253
19 1PMO PLR 2.5
20 2Z9V PXM 2.55102
21 1L5Y BEF 2.58065
22 1AJS PLA 2.6699
23 4LNL PLG 2.7027
24 4LNL 2BO 2.7027
25 4LNL 2BK 2.7027
26 3WGC PLG 2.93255
27 4AOA IK2 2.95455
28 4ZM4 PLP 2.95455
29 4JE5 PLP 2.95455
30 4JE5 PMP 2.95455
31 6ECG PM9 2.95455
32 4B98 PXG 2.95455
33 4ZM4 P3B 2.95455
34 5HZ9 5M8 2.96296
35 2R2N PMP 3.05882
36 4ZSY RW2 3.18182
37 3BS8 PMP 3.19635
38 1PCA CIT 3.22581
39 1K4M CIT 3.28639
40 2CJH AKG 3.34076
41 6FYQ PLP 3.40909
42 1WYV PLP AOA 3.40909
43 6C92 EQJ 3.45745
44 4RKC PMP 3.51759
45 3BWN PMP 3.58056
46 3BWN PMP PHE 3.58056
47 5BSH PRO 3.61011
48 2HHP FLC 3.63636
49 4ADC PLP 3.69458
50 4WXG 2BO 3.73832
51 3CQ5 PMP 3.79404
52 4UOX PLP 3.86364
53 4UOX PUT 3.86364
54 4UOX PLP PUT 3.86364
55 3ZRR PXG 3.90625
56 2X5F PLP 3.95349
57 1E5F PLP 3.9604
58 6C3C EJ1 4.31818
59 5W19 9TD 4.54545
60 1JS3 PLP 142 4.54545
61 3BGD PM6 4.61538
62 2HOX P1T 4.68384
63 3FQ8 PMP 4.77273
64 1K7T NAG GAL 4.83871
65 2ZL4 ALA ALA ALA ALA 5.10204
66 4HVK PMP 5.2356
67 5TDC NMM ILE PHE SER 5.26316
68 2JBH 5GP 5.33333
69 5YKT PMP 5.45455
70 4E3Q PMP 5.45455
71 1M32 PLP 5.46448
72 6DND PLP 5.68182
73 6CBO DOW 5.69476
74 5IWQ PLP 5.76037
75 6CD1 PLS 6.13636
76 6CD1 PLG 6.13636
77 5DDW 5B6 6.13636
78 1UU1 PMP HSA 6.56716
79 2OAT PFM 6.83371
80 1SFF IK2 7.04225
81 1ZC9 PMP 7.04545
82 1DJ9 KAM 7.29167
83 5H3A UMP 7.42049
84 2WK9 PLP 7.45501
85 2WK9 PLG 7.45501
86 3PD6 PMP 7.98005
87 3PDB PMP 7.98005
88 5AHO TLA 8.03571
89 1VJO PLP 8.90585
90 4WGF HX2 9.26829
91 5LUN OGA 9.375
92 1FC4 AKB PLP 9.47631
93 5X30 4LM 10.3015
94 5X30 7XF 10.3015
95 5X2Z 3LM 10.3015
96 4IYO 0JO 10.5793
97 4IY7 0JO 10.5793
98 4IY7 KOU 10.5793
99 4M2K PLP 10.5911
100 5TQZ GLC 10.6667
101 5VEQ PMP 10.7056
102 5WYF ILP 10.9091
103 2R5E QLP 11.4219
104 2R5C C6P 11.4219
105 1LW4 PLP 11.5274
106 1LW4 TLP 11.5274
107 1XI9 PLP 12.3153
108 2ZYJ PGU 12.8463
109 4P83 U5P 13.7363
110 2X5D PLP 13.835
111 4RJD TFP 15.1515
112 1GCK ASP PLP 16.6234
113 2ZC0 PMP 16.9533
114 5M3Z PLP 17.3367
115 5M3Z PY6 17.3367
116 5M3Z NLE 17.3367
117 1ELU PDA 19.7436
118 6EWR PMP 25.0585
119 2FNU PMP UD1 30.4
120 2PO3 T4K 32.3113
121 5K8B PDG 34.4913
122 1O69 X04 36.2944
123 1MDZ PLP 38.4224
124 1MDZ DCS 38.4224
125 3NUB UD0 38.4401
126 4K2M O1G 39.5455
127 3B8X G4M 40.2564
128 4ZAH T5K 40.6566
129 3FRK TQP 41.2869
130 2OGA PGU 42.3559
131 5U23 TQP 43.9791
132 3DR4 G4M 48.0818
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