Receptor
PDB id Resolution Class Description Source Keywords
5W70 2.1 Å EC: 2.6.1.100 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 EC: 2.6.1.100 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 1 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 1 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 1 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 (2D)
Ligand no: 1; Ligand: 9YM; Similar ligands found: 55
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 PP3 0.506173 0.80303
7 PDD 0.506173 0.80303
8 PDA 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 2BO 0.47619 0.830769
17 PMH 0.47619 0.780822
18 2BK 0.47619 0.830769
19 PLS 0.47619 0.875
20 TLP 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 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 0PR 0.456522 0.861538
34 ORX 0.455556 0.835821
35 PSZ 0.455556 0.736111
36 PGU 0.454545 0.820895
37 PDG 0.454545 0.820895
38 7XF 0.454545 0.820895
39 CBA 0.454545 0.820895
40 PL8 0.451613 0.77027
41 PE1 0.450549 0.835821
42 LPI 0.449438 0.763889
43 PY6 0.444444 0.774648
44 76U 0.444444 0.782609
45 HEY 0.444444 0.771429
46 DN9 0.442105 0.780822
47 PL4 0.44086 0.835821
48 N5F 0.43956 0.808824
49 3LM 0.43956 0.726027
50 PXG 0.425532 0.818182
51 KAM 0.416667 0.757143
52 AQ3 0.414141 0.850746
53 2QR 0.409449 0.75
54 LCS 0.402174 0.736842
55 OJQ 0.4 0.783784
Similar Ligands (3D)
Ligand no: 1; Ligand: 9YM; Similar ligands found: 6
No: Ligand Similarity coefficient
1 P3B 0.8839
2 L7N 0.8822
3 PLP 2KZ 0.8787
4 GAB PLP 0.8774
5 GBC PLP 0.8763
6 2B9 0.8635
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W70; Ligand: 9YM; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 5w70.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 34.4913
2 5K8B PDG 34.4913
3 3FRK TQP 35.1206
4 3FRK TQP 35.1206
5 3NUB UD0 38.9972
6 1B9I PXG 42.6966
7 3DR4 G4M 48.0818
8 3DR4 G4M 48.0818
9 3DR4 G4M 48.0818
10 3DR4 G4M 48.0818
Pocket No.: 2; Query (leader) PDB : 5W70; Ligand: 9YM; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 5w70.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 34.4913
2 5K8B PDG 34.4913
3 3FRK TQP 35.1206
4 3NUB UD0 38.9972
5 3NUB UD0 38.9972
6 1B9I PXG 42.6966
7 3DR4 G4M 48.0818
8 3DR4 G4M 48.0818
9 3DR4 G4M 48.0818
10 3DR4 G4M 48.0818
APoc FAQ
Feedback