Receptor
PDB id Resolution Class Description Source Keywords
6Q8B 2.2 Å EC: 6.1.1.4 NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH (L-LEUCYL)-SULFAMOYL)N3-METHYLURIDINE NEISSERIA GONORRHOEAE PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA SYNTHETASE L
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
L3U A:901;
 Valid;
 none;
 submit data
450.464 C16 H26 N4 O9 S CC(C)...
EDO A:903;
A:904;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
MG A:905;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
ZN A:902;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6YKL 2.27 Å EC: 6.1.1.4 NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH 11K NEISSERIA GONORRHOEAE PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA SYNTHETASE L
Ref.: SYNTHESIS AND STRUCTURE-ACTIVITY STUDIES OF NOVEL ANHYDROHEXITOL-BASED LEUCYL-TRNA SYNTHETASE INHIBIT EUR.J.MED.CHEM. 13021 2020
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6YKW Ki = 1260.73 nM OVZ C25 H40 N6 O7 S CC(C)C[C@@....
2 6YKS Ki = 108.35 nM OVT C25 H39 N5 O7 S CC(C)C[C@@....
3 6Q8B - L3U C16 H26 N4 O9 S CC(C)C[C@@....
4 6YKT Ki = 387.66 nM OVN C21 H39 N5 O8 S CC(C)C[C@@....
5 6YKU Ki = 17.83 nM OVB C24 H34 F3 N5 O8 S CC(C)C[C@@....
6 6YKV Ki = 31.62 nM OVQ C22 H34 N6 O7 S CC(C)C[C@@....
7 7AP2 - RRW C19 H29 N5 O8 S CC(C)C[C@@....
8 6YKO Ki = 5.51 nM OW5 C28 H45 N5 O7 S CCCCCc1ccc....
9 6YKX Ki = 182.35 nM OW2 C26 H41 N7 O8 S CC(C)C[C@@....
10 6Q8A - HQ5 C15 H25 N5 O8 S CC(C)C[C@@....
11 6Q8C - LSU C15 H24 N4 O9 S CC(C)C[C@@....
12 6YKK Ki = 30.94 nM OVK C20 H30 N6 O7 S CC(C)C[C@@....
13 7A0P Ki = 31.28 nM QTW C25 H38 N6 O8 S CC(C)C[C@@....
14 6Q89 - LSS C16 H25 N7 O7 S CC(C)C[C@@....
15 6YKQ Ki = 52.36 nM OVW C25 H47 N5 O7 S CCCCCCCCc1....
16 6YKL Ki = 2.48 nM OVH C23 H35 N5 O7 S CC(C)C[C@@....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6YKW Ki = 1260.73 nM OVZ C25 H40 N6 O7 S CC(C)C[C@@....
2 6YKS Ki = 108.35 nM OVT C25 H39 N5 O7 S CC(C)C[C@@....
3 6Q8B - L3U C16 H26 N4 O9 S CC(C)C[C@@....
4 6YKT Ki = 387.66 nM OVN C21 H39 N5 O8 S CC(C)C[C@@....
5 6YKU Ki = 17.83 nM OVB C24 H34 F3 N5 O8 S CC(C)C[C@@....
6 6YKV Ki = 31.62 nM OVQ C22 H34 N6 O7 S CC(C)C[C@@....
7 7AP2 - RRW C19 H29 N5 O8 S CC(C)C[C@@....
8 6YKO Ki = 5.51 nM OW5 C28 H45 N5 O7 S CCCCCc1ccc....
9 6YKX Ki = 182.35 nM OW2 C26 H41 N7 O8 S CC(C)C[C@@....
10 6Q8A - HQ5 C15 H25 N5 O8 S CC(C)C[C@@....
11 6Q8C - LSU C15 H24 N4 O9 S CC(C)C[C@@....
12 6YKK Ki = 30.94 nM OVK C20 H30 N6 O7 S CC(C)C[C@@....
13 7A0P Ki = 31.28 nM QTW C25 H38 N6 O8 S CC(C)C[C@@....
14 6Q89 - LSS C16 H25 N7 O7 S CC(C)C[C@@....
15 6YKQ Ki = 52.36 nM OVW C25 H47 N5 O7 S CCCCCCCCc1....
16 6YKL Ki = 2.48 nM OVH C23 H35 N5 O7 S CC(C)C[C@@....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6YKW Ki = 1260.73 nM OVZ C25 H40 N6 O7 S CC(C)C[C@@....
2 6YKS Ki = 108.35 nM OVT C25 H39 N5 O7 S CC(C)C[C@@....
3 6Q8B - L3U C16 H26 N4 O9 S CC(C)C[C@@....
4 6YKT Ki = 387.66 nM OVN C21 H39 N5 O8 S CC(C)C[C@@....
5 6YKU Ki = 17.83 nM OVB C24 H34 F3 N5 O8 S CC(C)C[C@@....
6 6YKV Ki = 31.62 nM OVQ C22 H34 N6 O7 S CC(C)C[C@@....
7 7AP2 - RRW C19 H29 N5 O8 S CC(C)C[C@@....
8 6YKO Ki = 5.51 nM OW5 C28 H45 N5 O7 S CCCCCc1ccc....
9 6YKX Ki = 182.35 nM OW2 C26 H41 N7 O8 S CC(C)C[C@@....
10 6Q8A - HQ5 C15 H25 N5 O8 S CC(C)C[C@@....
11 6Q8C - LSU C15 H24 N4 O9 S CC(C)C[C@@....
12 6YKK Ki = 30.94 nM OVK C20 H30 N6 O7 S CC(C)C[C@@....
13 7A0P Ki = 31.28 nM QTW C25 H38 N6 O8 S CC(C)C[C@@....
14 6Q89 - LSS C16 H25 N7 O7 S CC(C)C[C@@....
15 6YKQ Ki = 52.36 nM OVW C25 H47 N5 O7 S CCCCCCCCc1....
16 6YKL Ki = 2.48 nM OVH C23 H35 N5 O7 S CC(C)C[C@@....
17 1OBC - NVA 2AD n/a n/a
18 1H3N - LEU LMS n/a n/a
19 2V0C - LEU LMS n/a n/a
20 1OBH - NVA LMS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: L3U; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 L3U 1 1
2 FZT 0.814815 0.940476
3 Y3U 0.725275 0.929412
4 LSU 0.655556 0.987805
5 HQ5 0.648352 0.952941
6 FZK 0.510417 0.916667
7 FZQ 0.505155 0.885057
8 YSU 0.471698 0.905882
9 YSC 0.46729 0.875
10 OVK 0.428571 0.815217
11 LSS 0.425926 0.876405
12 RRW 0.419643 0.865169
Similar Ligands (3D)
Ligand no: 1; Ligand: L3U; Similar ligands found: 12
No: Ligand Similarity coefficient
1 LEU LMS 0.9442
2 NVA LMS 0.9310
3 5CA 0.9036
4 C2G 0.8976
5 7XL 0.8910
6 MSP 0.8873
7 ATP 0.8814
8 MOD 0.8782
9 ME8 0.8771
10 UTP 0.8714
11 53H 0.8665
12 52H 0.8617
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6YKL; Ligand: OVH; 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: 6ykl.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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