Receptor
PDB id Resolution Class Description Source Keywords
6HB6 1.92 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L SULFAMOYL-URIDINE ESCHERICHIA COLI (STRAIN B / BL21-DE3)ORGANISM_TAXID: 469008 PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA AMINOACYLATIO
Ref.: COMPARATIVE ANALYSIS OF PYRIMIDINE SUBSTITUTED AMINOACYL-SULFAMOYL NUCLEOSIDES AS POTENTIAL INHIBI TARGETING CLASS I AMINOACYL-TRNA SYNTHETASES. EUR.J.MED.CHEM. V. 173 154 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:502;
A:503;
B:502;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
YSU B:501;
A:501;
 Valid;
Valid;
 none;
none;
 submit data
486.453 C18 H22 N4 O10 S c1cc(...
CL A:504;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HB5 1.88 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L SULFAMOYL-CYTIDINE ESCHERICHIA COLI (STRAIN B / BL21-DE3)ORGANISM_TAXID: 469008 PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA AMINOACYLATIO
Ref.: COMPARATIVE ANALYSIS OF PYRIMIDINE SUBSTITUTED AMINOACYL-SULFAMOYL NUCLEOSIDES AS POTENTIAL INHIBI TARGETING CLASS I AMINOACYL-TRNA SYNTHETASES. EUR.J.MED.CHEM. V. 173 154 2019
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
2 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
3 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
4 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
5 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1WQ4 - TYR C9 H11 N O3 c1cc(ccc1C....
2 2YXN - AZY C9 H10 N4 O3 c1cc(c(cc1....
3 1WQ3 - IYR C9 H10 I N O3 c1cc(c(cc1....
4 1X8X - TYR C9 H11 N O3 c1cc(ccc1C....
5 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
6 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
7 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
8 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
9 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
10 1TYB - TYR C9 H11 N O3 c1cc(ccc1C....
11 4TS1 Kd = 11.6 uM TYR C9 H11 N O3 c1cc(ccc1C....
12 1TYD - TYR C9 H11 N O3 c1cc(ccc1C....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1WQ4 - TYR C9 H11 N O3 c1cc(ccc1C....
2 2YXN - AZY C9 H10 N4 O3 c1cc(c(cc1....
3 1WQ3 - IYR C9 H10 I N O3 c1cc(c(cc1....
4 1X8X - TYR C9 H11 N O3 c1cc(ccc1C....
5 1Y42 - TYR C9 H11 N O3 c1cc(ccc1C....
6 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
7 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
8 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
9 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
10 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
11 1JIL ic50 = 4 nM 485 C17 H24 N2 O8 C[C@@H]1[C....
12 2PID - YSA C19 H23 N7 O8 S c1cc(ccc1C....
13 1TYB - TYR C9 H11 N O3 c1cc(ccc1C....
14 4TS1 Kd = 11.6 uM TYR C9 H11 N O3 c1cc(ccc1C....
15 1TYD - TYR C9 H11 N O3 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: YSU; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 YSU 1 1
2 FZK 0.735632 0.939024
3 LSU 0.703297 0.916667
4 YSC 0.697917 0.963855
5 Y3U 0.680412 0.97561
6 FZQ 0.490196 0.905882
7 FZT 0.485437 0.916667
8 U5P 0.483516 0.756098
9 U 0.483516 0.756098
10 HQ5 0.471698 0.885057
11 L3U 0.471698 0.905882
12 44P 0.468085 0.741176
13 2KH 0.464646 0.75
14 YSA 0.46087 0.895349
15 UDP 0.453608 0.746988
16 UDP UDP 0.453608 0.743902
17 RRB 0.445378 0.883721
18 UNP 0.441176 0.75
19 UTP 0.44 0.746988
20 URI 0.436782 0.682927
21 U5F 0.435644 0.746988
22 660 0.435185 0.761905
23 URM 0.435185 0.761905
24 UDH 0.425926 0.738636
25 UDM 0.422414 0.752941
26 CJB 0.422222 0.670732
27 UPG 0.422018 0.75
28 UFM 0.422018 0.75
29 GDU 0.422018 0.75
30 UPU 0.419048 0.768293
31 Y6W 0.418182 0.735632
32 AWU 0.418182 0.75
33 USQ 0.415929 0.869048
34 UGB 0.415929 0.759036
35 UGA 0.415929 0.759036
36 F5G 0.413223 0.741176
37 F5P 0.413223 0.752941
38 UD4 0.413223 0.752941
39 UPP 0.412844 0.792683
40 UDP GAL 0.410714 0.729412
41 UD7 0.408333 0.741176
42 MJZ 0.404959 0.77381
43 UD1 0.403361 0.741176
44 UD2 0.403361 0.741176
45 U4S 0.402062 0.643678
46 EEB 0.401575 0.724138
47 UGF 0.4 0.724138
48 G3N 0.4 0.795181
Similar Ligands (3D)
Ligand no: 1; Ligand: YSU; Similar ligands found: 3
No: Ligand Similarity coefficient
1 TYR AMP 0.9097
2 C2G 0.8644
3 CDC 0.8643
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6HB5; Ligand: YSC; 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: 6hb5.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6HB5; Ligand: YSC; 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: 6hb5.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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