Receptor
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
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)...
YSC A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
485.468 C18 H23 N5 O9 S c1cc(...
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: YSC; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 YSC 1 1
2 FZQ 0.738636 0.941176
3 HQ5 0.706522 0.91954
4 YSU 0.697917 0.963855
5 Y3U 0.673469 0.941176
6 C 0.5 0.776471
7 CAR 0.5 0.776471
8 C5P 0.5 0.776471
9 FZK 0.490196 0.905882
10 YSA 0.482456 0.886364
11 FZT 0.480769 0.885057
12 RRB 0.478632 0.853933
13 LSU 0.471698 0.885057
14 CDP 0.469388 0.767442
15 CDP MG 0.469388 0.764706
16 L3U 0.46729 0.875
17 HF4 0.455446 0.767442
18 CTP 0.455446 0.767442
19 CTN 0.454545 0.694118
20 AR3 0.454545 0.694118
21 C2G 0.45283 0.77907
22 7XL 0.451923 0.770115
23 I5A 0.449438 0.682353
24 2TM 0.446602 0.761364
25 0RC 0.438095 0.772727
26 CDM 0.432432 0.736264
27 C5G 0.428571 0.770115
28 PMT 0.427419 0.723404
29 A7R 0.425 0.781609
30 1AA 0.420168 0.764045
31 CXY 0.412281 0.790698
32 CDC 0.410714 0.705263
33 CDP RB0 0.408696 0.75
34 NVG 0.405172 0.695652
35 V12 0.4 0.711111
Similar Ligands (3D)
Ligand no: 1; Ligand: YSC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 TYR AMP 0.9093
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
APoc FAQ
Feedback