Receptor
PDB id Resolution Class Description Source Keywords
5W70 2.1 Å NON-ENZYME: OTHER X-RAY STRUCTURE OF RBMB FROM STREPTOMYCES RIBOSIDIFICUS STREPTOMYCES RIBOSIDIFICUS RIBOSTAMYCIN AMINOTRANSFERASE AMINOGLYCOSIDE AMINOCYCLITOANTIBIOTIC 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
EDO B:502;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
9YM A:501;
B:501;
Valid;
Valid;
none;
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
5W70 2.1 Å NON-ENZYME: OTHER X-RAY STRUCTURE OF RBMB FROM STREPTOMYCES RIBOSIDIFICUS STREPTOMYCES RIBOSIDIFICUS RIBOSTAMYCIN AMINOTRANSFERASE AMINOGLYCOSIDE AMINOCYCLITOANTIBIOTIC TRANSFERASE
Ref.: THE STRUCTURE OF RBMB FROM STREPTOMYCES RIBOSIDIFIC AMINOTRANSFERASE INVOLVED IN THE BIOSYNTHESIS OF RIBOSTAMYCIN. PROTEIN SCI. V. 26 1886 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5W70 - 9YM C14 H24 N3 O8 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5W70 - 9YM C14 H24 N3 O8 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: 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 : 5W70; Ligand: 9YM; Similar sites found: 88
This union binding pocket(no: 1) in the query (biounit: 5w70.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5G4J EXT 0.0004584 0.4532 1.1236
2 5KGS 6SR 0.001736 0.45459 1.34831
3 1MLY ACZ PLP 0.004645 0.40188 1.6317
4 2FN1 PYR 0.02507 0.4074 1.83066
5 3EI9 PL6 0.001624 0.41007 1.85185
6 3FQ8 PMP 0.001256 0.43601 1.87354
7 1ZC9 PMP 0.0007734 0.44339 2.02247
8 5GVL PLG 0.0007071 0.46829 2.0362
9 5GVL GI8 0.0007071 0.46829 2.0362
10 3B1E P1T 0.01017 0.40538 2.04082
11 3VP6 HLD 0.004248 0.41484 2.15264
12 1UU1 PMP HSA 0.001199 0.42559 2.68657
13 4UHO PLP 0.002106 0.45733 2.69663
14 1M32 PLP 0.00264 0.45319 2.73224
15 3PD6 PMP 0.00006278 0.52048 2.74314
16 3PDB PMP 0.00004598 0.46039 2.74314
17 4L6H HCS 0.0192 0.41038 2.92135
18 1PMO PLR 0.002757 0.43612 3.14607
19 4JE5 PLP 0.003712 0.43461 3.14607
20 4JE5 PMP 0.003923 0.43344 3.14607
21 2ZC0 PMP 0.00003482 0.50717 3.1941
22 2R2N PMP 0.0004722 0.47237 3.29412
23 3E2Y PMP 0.0001979 0.49022 3.41463
24 1U08 PLP 0.0001718 0.4993 3.62694
25 5IWQ PLP 0.0005414 0.46956 3.68664
26 5DJ3 5DK 0.002024 0.41682 3.7234
27 1FC4 AKB PLP 0.0005238 0.4507 3.74065
28 2WK9 PLG 0.00003885 0.51569 3.82022
29 2WK9 PLP 0.00003859 0.51251 3.82022
30 4ZM4 PLP 0.0002517 0.47964 3.82022
31 2HOX P1T 0.002379 0.4223 3.82022
32 4ZM4 P3B 0.006004 0.40156 3.82022
33 4UOX PLP 0.0003474 0.47867 4.04494
34 4UOX PUT 0.004445 0.41801 4.04494
35 4UOX PLP PUT 0.008832 0.40099 4.04494
36 3CQ5 PMP 0.001294 0.46813 4.06504
37 1K4M CIT 0.02765 0.41275 4.22535
38 1AJS PLA 0.0005188 0.45253 4.61165
39 1WB4 SXX 0.00675 0.43303 4.7191
40 4ZSY RW2 0.001826 0.41749 4.7191
41 2OAT PFM 0.009093 0.40043 4.7836
42 4RKC PMP 0.0003691 0.47197 5.02513
43 4BA5 PXG 0.0002137 0.47752 5.39326
44 1DJ9 KAM 0.00003436 0.51333 5.8427
45 4FL0 PLP 0.001129 0.45446 5.8427
46 5WYF ILP 0.0008639 0.43721 6.06742
47 4ADC PLP 0.002502 0.401 6.15764
48 4E3Q PMP 0.0001159 0.50758 6.51685
49 1WYV PLP AOA 0.001949 0.43001 6.51685
50 2X5D PLP 0.01743 0.4102 6.5534
51 3BWN PMP 0.0001158 0.50122 7.16113
52 3BWN PMP PHE 0.0007749 0.43312 7.16113
53 1ELU PDA 0.006615 0.40308 7.17949
54 4AOA IK2 0.000773 0.45232 7.19101
55 5X30 4LM 0.00009291 0.48836 8.0402
56 5X30 7XF 0.00009324 0.48307 8.0402
57 5X2Z 3LM 0.000141 0.48071 8.0402
58 3WGC PLG 0.0001034 0.49174 8.21114
59 5G09 6DF 0.002659 0.41654 8.31461
60 4R5Z PMP 0.001014 0.42286 8.71935
61 2R5C C6P 0.001121 0.43241 9.55711
62 2R5E QLP 0.001133 0.43223 9.55711
63 1DFO PLG 0.0000868 0.47941 10.5516
64 2ZYJ PGU 0.0007832 0.40549 10.5793
65 2X5F PLP 0.0002794 0.48907 10.7865
66 1GDE GLU PLP 0.003272 0.41631 12.5843
67 1SFF IK2 0.001213 0.43097 12.6761
68 2FYF PLP 0.003231 0.44251 14.1573
69 1LW4 TLP 0.0004291 0.44434 14.4092
70 1LW4 PLP 0.0002541 0.4413 14.4092
71 1XI9 PLP 0.003405 0.44138 15.0246
72 1GCK ASP PLP 0.0006791 0.44163 15.5844
73 4WXG 2BO 0.000128 0.44935 17.0561
74 4IY7 KOU 0.0005019 0.44718 23.5955
75 4IY7 0JO 0.0005088 0.44693 23.5955
76 4IYO 0JO 0.0005569 0.44527 23.5955
77 2PO3 T4K 0.00000005368 0.49563 25.2358
78 1O69 X04 0.00000008343 0.42724 29.4416
79 2FNU PMP UD1 0.00000000861 0.5017 31.2
80 4ZAH T5K 0.0000000192 0.55729 32.8283
81 5K8B PDG 0.000000000191 0.7259 34.4913
82 3B8X G4M 0.00000007604 0.49658 37.1795
83 1MDZ DCS 0.0000003059 0.47703 38.1679
84 1MDZ PLP 0.0000008695 0.46928 38.1679
85 3NUB UD0 0.000000002008 0.56011 38.9972
86 2OGA PGU 0.00000002498 0.6323 40.1003
87 5U23 TQP 0.000000007583 0.67891 44.2697
88 3DR4 G4M 0.000000003448 0.50151 48.0818
Pocket No.: 2; Query (leader) PDB : 5W70; Ligand: 9YM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5w70.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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