Receptor
PDB id Resolution Class Description Source Keywords
6Q8C 2.31 Å EC: 6.1.1.4 NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH (L-LEUCYL)-SULFAMOYL)URIDINE 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
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...
LSU A:901;
 Valid;
 none;
 submit data
436.437 C15 H24 N4 O9 S CC(C)...
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: LSU; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 LSU 1 1
2 FZK 0.8 0.927711
3 YSU 0.703297 0.916667
4 HQ5 0.674157 0.964286
5 L3U 0.655556 0.987805
6 FZQ 0.526316 0.895349
7 FZT 0.520833 0.928571
8 U 0.505882 0.746988
9 U5P 0.505882 0.746988
10 44P 0.488636 0.732558
11 2KH 0.483871 0.741176
12 URI 0.475 0.674699
13 UDP UDP 0.472527 0.73494
14 UDP 0.472527 0.738095
15 YSC 0.471698 0.885057
16 Y3U 0.471698 0.917647
17 UNP 0.458333 0.741176
18 UTP 0.457447 0.738095
19 U5F 0.452632 0.738095
20 UDH 0.441176 0.730337
21 CJB 0.440476 0.642857
22 660 0.436893 0.732558
23 GDU 0.436893 0.72093
24 UFM 0.436893 0.72093
25 URM 0.436893 0.732558
26 UPG 0.436893 0.72093
27 UDM 0.436364 0.744186
28 UPU 0.434343 0.738095
29 USQ 0.429907 0.837209
30 LSS 0.429907 0.886364
31 UD1 0.428571 0.732558
32 UD2 0.428571 0.732558
33 UDP GAL 0.424528 0.701149
34 OVK 0.419643 0.824176
35 Y6W 0.419048 0.707865
36 AWU 0.419048 0.741176
37 U4S 0.417582 0.636364
38 MJZ 0.417391 0.764706
39 UGA 0.416667 0.729412
40 UGB 0.416667 0.729412
41 EPZ 0.416667 0.744186
42 U1S 0.415842 0.655556
43 F5G 0.413793 0.752941
44 UD4 0.413793 0.764706
45 F5P 0.413793 0.764706
46 UPP 0.413462 0.72093
47 EEB 0.413223 0.735632
48 G3N 0.412844 0.764706
49 UGF 0.412844 0.696629
50 UAD 0.411215 0.741176
51 UDX 0.411215 0.741176
52 UPF 0.411215 0.688889
53 U2F 0.411215 0.688889
54 UFG 0.411215 0.688889
55 RRW 0.410714 0.875
56 HP7 0.408696 0.741176
57 UD7 0.408696 0.752941
58 U3S 0.408602 0.636364
59 U2S 0.408602 0.647727
60 HWU 0.401709 0.735632
61 12V 0.401709 0.735632
62 UDZ 0.4 0.722222
63 UUA 0.4 0.60241
Similar Ligands (3D)
Ligand no: 1; Ligand: LSU; Similar ligands found: 0
No: Ligand Similarity coefficient
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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