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 922 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: 55
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 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Ligand no: 2; Ligand: 9YM; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 9YM 1 1
2 DCS 0.535714 0.797297
3 5PA 0.512195 0.835821
4 IN5 0.506329 0.828125
5 PLG 0.506329 0.818182
6 PDD 0.506173 0.80303
7 PP3 0.506173 0.80303
8 PDA 0.506173 0.80303
9 PLA 0.5 0.797101
10 33P 0.5 0.787879
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 PLS 0.47619 0.875
17 PMH 0.47619 0.780822
18 2BO 0.47619 0.830769
19 TLP 0.47619 0.830769
20 2BK 0.47619 0.830769
21 EA5 0.47191 0.811594
22 ILP 0.471264 0.779412
23 7TS 0.471264 0.74026
24 PPD 0.470588 0.846154
25 C6P 0.470588 0.846154
26 GT1 0.466667 0.723077
27 PL2 0.465909 0.797101
28 QLP 0.465909 0.8
29 PY5 0.465116 0.797101
30 7B9 0.457447 0.802817
31 RW2 0.456522 0.785714
32 PSZ 0.455556 0.736111
33 ORX 0.455556 0.835821
34 PGU 0.454545 0.820895
35 7XF 0.454545 0.820895
36 CBA 0.454545 0.820895
37 PDG 0.454545 0.820895
38 PL8 0.451613 0.77027
39 PE1 0.450549 0.835821
40 HEY 0.444444 0.771429
41 PY6 0.444444 0.774648
42 76U 0.444444 0.782609
43 PL4 0.44086 0.835821
44 N5F 0.43956 0.808824
45 3LM 0.43956 0.726027
46 PXG 0.425532 0.818182
47 KAM 0.416667 0.757143
48 AQ3 0.414141 0.850746
49 2QR 0.409449 0.75
50 LCS 0.402174 0.736842
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W71; Ligand: 9YM; Similar sites found: 85
This union binding pocket(no: 1) in the query (biounit: 5w71.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1MLY ACZ PLP 0.009967 0.41977 1.3986
2 4UHO PLP 0.002817 0.47726 1.59091
3 2FYF PLP 0.008481 0.44629 1.75879
4 4BA5 PXG 0.0005292 0.48874 1.81818
5 5G4J EXT 0.002279 0.44981 1.81818
6 1OXO IK2 0.0003036 0.41716 1.99501
7 4YIW NCD 0.03881 0.41554 2.04545
8 5LTJ BEF 0.03722 0.4154 2.04545
9 3EI9 PL6 0.00789 0.4124 2.27273
10 1PMO PLR 0.004199 0.45323 2.5
11 1AJS PLA 0.00177 0.44062 2.6699
12 3B1E P1T 0.03266 0.40431 2.80612
13 3WGC PLG 0.0004214 0.49355 2.93255
14 4ZM4 PLP 0.0006663 0.48875 2.95455
15 4AOA IK2 0.002112 0.45944 2.95455
16 4JE5 PLP 0.006661 0.44732 2.95455
17 4JE5 PMP 0.007774 0.44381 2.95455
18 4B98 PXG 0.009492 0.42409 2.95455
19 4ZM4 P3B 0.01762 0.4052 2.95455
20 2R2N PMP 0.001165 0.48157 3.05882
21 4ZSY RW2 0.004918 0.42747 3.18182
22 1PCA CIT 0.04039 0.42656 3.22581
23 1WYV PLP AOA 0.007377 0.42933 3.40909
24 5DJ3 5DK 0.007807 0.42475 3.45745
25 4RKC PMP 0.001089 0.47813 3.51759
26 3BWN PMP 0.001223 0.4805 3.58056
27 3BWN PMP PHE 0.007177 0.42006 3.58056
28 2HHP FLC 0.04861 0.43154 3.63636
29 4ADC PLP 0.006638 0.41566 3.69458
30 4WXG 2BO 0.0009797 0.45177 3.73832
31 3CQ5 PMP 0.005872 0.45981 3.79404
32 4UOX PLP 0.000704 0.4927 3.86364
33 4UOX PUT 0.007533 0.43249 3.86364
34 4UOX PLP PUT 0.0132 0.41722 3.86364
35 2X5F PLP 0.0007579 0.49649 3.95349
36 1JS3 PLP 142 0.01531 0.411 4.54545
37 2HOX P1T 0.01504 0.41137 4.68384
38 1K7T NAG GAL 0.03261 0.40098 4.83871
39 2ZL4 ALA ALA ALA ALA 0.0443 0.41141 5.10204
40 5TDC NMM ILE PHE SER 0.03141 0.41542 5.26316
41 4E3Q PMP 0.0003338 0.51502 5.45455
42 1M32 PLP 0.02022 0.42934 5.46448
43 5IWQ PLP 0.002654 0.46337 5.76037
44 5DDW 5B6 0.001654 0.4488 6.13636
45 1UU1 PMP HSA 0.008568 0.41659 6.56716
46 2OAT PFM 0.02532 0.40359 6.83371
47 1SFF IK2 0.003709 0.43637 7.04225
48 1ZC9 PMP 0.001 0.46655 7.04545
49 1DJ9 KAM 0.0005001 0.48993 7.29167
50 2WK9 PLP 0.004021 0.40893 7.45501
51 2WK9 PLG 0.00502 0.40055 7.45501
52 3PD6 PMP 0.0001149 0.53911 7.98005
53 3PDB PMP 0.0002322 0.5172 7.98005
54 5LUN OGA 0.04402 0.40422 9.375
55 1FC4 AKB PLP 0.002487 0.44804 9.47631
56 5X30 4LM 0.0009994 0.47082 10.3015
57 5X30 7XF 0.00102 0.46616 10.3015
58 5X2Z 3LM 0.003956 0.41964 10.3015
59 4IYO 0JO 0.002739 0.44242 10.5793
60 4IY7 0JO 0.00291 0.44121 10.5793
61 4IY7 KOU 0.003065 0.44018 10.5793
62 3E2Y PMP 0.0008181 0.48938 10.7317
63 5WYF ILP 0.004307 0.43339 10.9091
64 2R5E QLP 0.005324 0.42916 11.4219
65 2R5C C6P 0.006275 0.42588 11.4219
66 1XI9 PLP 0.01546 0.43232 12.3153
67 2X5D PLP 0.04612 0.40964 13.835
68 4RJD TFP 0.03504 0.41239 15.1515
69 1GCK ASP PLP 0.003469 0.43771 16.6234
70 2ZC0 PMP 0.0002267 0.50157 16.9533
71 1ELU PDA 0.007694 0.42505 19.7436
72 2FNU PMP UD1 0.000006293 0.4961 30.4
73 2PO3 T4K 0.000007458 0.50058 32.3113
74 5K8B PDG 0.00000000115 0.71736 34.4913
75 1O69 X04 0.000000000007288 0.63118 36.2944
76 1MDZ PLP 0.000009034 0.50496 38.4224
77 1MDZ DCS 0.000007914 0.50334 38.4224
78 3NUB UD0 0.0000002496 0.56905 38.4401
79 4K2M O1G 0.000000001179 0.71689 39.5455
80 3B8X G4M 0.000002201 0.52014 40.2564
81 4ZAH T5K 0.0000004246 0.57513 40.6566
82 3FRK TQP 0.00000004125 0.59924 41.2869
83 2OGA PGU 0.00000002039 0.66976 42.3559
84 5U23 TQP 0.0000002191 0.57123 43.9791
85 3DR4 G4M 0.000003323 0.49893 48.0818
Pocket No.: 2; Query (leader) PDB : 5W71; Ligand: PLP; Similar sites found: 87
This union binding pocket(no: 2) in the query (biounit: 5w71.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1MLY ACZ PLP 0.0006623 0.42437 1.3986
2 4UHO PLP 0.0007161 0.47689 1.59091
3 1DFO PLG 0.0001472 0.47954 1.67866
4 2FYF PLP 0.002166 0.44705 1.75879
5 4BA5 PXG 0.0001234 0.4835 1.81818
6 5G4J EXT 0.0006477 0.4386 1.81818
7 5LTJ BEF 0.01463 0.41215 2.04545
8 4YIW NCD 0.02202 0.40264 2.04545
9 3EI9 PL6 0.0009345 0.41074 2.27273
10 1PMO PLR 0.001318 0.44707 2.5
11 1AJS PLA 0.0002865 0.42857 2.6699
12 3B1E P1T 0.009922 0.40215 2.80612
13 3WGC PLG 0.00007226 0.49386 2.93255
14 4DOE CBK 0.01321 0.4172 2.94737
15 4ZM4 PLP 0.0001366 0.48714 2.95455
16 4AOA IK2 0.000697 0.44998 2.95455
17 4JE5 PLP 0.003195 0.43376 2.95455
18 4JE5 PMP 0.003403 0.43245 2.95455
19 4B98 PXG 0.003675 0.41387 2.95455
20 4ZM4 P3B 0.003338 0.40319 2.95455
21 2R2N PMP 0.0003665 0.47304 3.05882
22 4ZSY RW2 0.0007679 0.4236 3.18182
23 1K4M CIT 0.03422 0.4018 3.28639
24 1WYV PLP AOA 0.00269 0.41978 3.40909
25 5DJ3 5DK 0.0015 0.42396 3.45745
26 4RKC PMP 0.0003284 0.46976 3.51759
27 3BWN PMP 0.0002877 0.47795 3.58056
28 3BWN PMP PHE 0.001104 0.41787 3.58056
29 2HHP FLC 0.01725 0.45072 3.63636
30 4ADC PLP 0.0002857 0.4781 3.69458
31 4WXG 2BO 0.0001892 0.43195 3.73832
32 3CQ5 PMP 0.003553 0.44174 3.79404
33 4UOX PLP 0.0001362 0.49313 3.86364
34 4UOX PUT 0.002348 0.42646 3.86364
35 4UOX PLP PUT 0.004195 0.41136 3.86364
36 2X5F PLP 0.0005125 0.47185 3.95349
37 1WB4 SXX 0.004268 0.44053 4.0404
38 1JS3 PLP 142 0.003592 0.40774 4.54545
39 1W6F ISZ 0.02131 0.40558 4.67626
40 2HOX P1T 0.005009 0.40308 4.68384
41 3FQ8 PMP 0.00096 0.44936 4.77273
42 5TDC NMM ILE PHE SER 0.009271 0.41777 5.26316
43 4E3Q PMP 0.00008558 0.50909 5.45455
44 1M32 PLP 0.005111 0.43418 5.46448
45 5IWQ PLP 0.0006446 0.46158 5.76037
46 5DDW 5B6 0.0009071 0.41888 6.13636
47 1UU1 PMP HSA 0.002135 0.40798 6.56716
48 1SFF IK2 0.0006784 0.43086 7.04225
49 1ZC9 PMP 0.0001537 0.46467 7.04545
50 1DJ9 KAM 0.0001515 0.47952 7.29167
51 2WK9 PLP 0.0001198 0.40669 7.45501
52 3PD6 PMP 0.00003108 0.53016 7.98005
53 3PDB PMP 0.00004272 0.51666 7.98005
54 5LUN OGA 0.01232 0.40559 9.375
55 1FC4 AKB PLP 0.0007204 0.43745 9.47631
56 5X30 4LM 0.0003756 0.45707 10.3015
57 5X30 7XF 0.0002782 0.45536 10.3015
58 5X2Z 3LM 0.0003937 0.4138 10.3015
59 4IY7 KOU 0.001272 0.42291 10.5793
60 4IY7 0JO 0.001342 0.42165 10.5793
61 4IYO 0JO 0.00136 0.42139 10.5793
62 3E2Y PMP 0.0002567 0.48027 10.7317
63 5WYF ILP 0.001138 0.42171 10.9091
64 2R5E QLP 0.001546 0.41806 11.4219
65 2R5C C6P 0.001969 0.41383 11.4219
66 1LW4 TLP 0.0001815 0.47323 11.5274
67 1LW4 PLP 0.0001198 0.47127 11.5274
68 1XI9 PLP 0.00645 0.42372 12.3153
69 2X5D PLP 0.01819 0.40565 13.835
70 4RJD TFP 0.01204 0.41239 15.1515
71 1GCK ASP PLP 0.0007729 0.43034 16.6234
72 2ZC0 PMP 0.00006841 0.4893 16.9533
73 1ELU PDA 0.001543 0.42419 19.7436
74 2FNU PMP UD1 0.000000001279 0.50615 30.4
75 2PO3 T4K 0.00000001626 0.4919 32.3113
76 5K8B PDG 0.000000000009419 0.70788 34.4913
77 1O69 X04 0.00000001191 0.43205 36.2944
78 1MDZ PLP 0.00000001651 0.50325 38.4224
79 1MDZ DCS 0.00000001837 0.49479 38.4224
80 3NUB UD0 0.00000000003091 0.58653 38.4401
81 4K2M O1G 0.00000000001096 0.70551 39.5455
82 3B8X G4M 0.00000001477 0.49615 40.2564
83 4ZAH T5K 0.000000000471 0.58618 40.6566
84 3FRK TQP 0.00000000006588 0.57691 41.2869
85 2OGA PGU 0.0000000002602 0.66972 42.3559
86 5U23 TQP 0.0000000001755 0.56437 43.9791
87 3DR4 G4M 0.0000000004806 0.49953 48.0818
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