Receptor
PDB id Resolution Class Description Source Keywords
6HB7 1.9 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L SULFAMOYL-N3-METHYLURIDINE ESCHERICHIA COLI BL21(DE3) 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;
A:504;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
Y3U A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
500.48 C19 H24 N4 O10 S CN1C(...
CL A:505;
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: Y3U; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 Y3U 1 1
2 FZT 0.75 0.940476
3 L3U 0.725275 0.929412
4 YSU 0.680412 0.97561
5 YSC 0.673469 0.941176
6 FZK 0.475728 0.916667
7 LSU 0.471698 0.917647
8 FZQ 0.471154 0.885057
9 HQ5 0.46729 0.886364
10 YSA 0.456897 0.875
11 RRB 0.453782 0.863636
Similar Ligands (3D)
Ligand no: 1; Ligand: Y3U; Similar ligands found: 2
No: Ligand Similarity coefficient
1 TYR AMP 0.9340
2 TYM 0.8792
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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