Receptor
PDB id Resolution Class Description Source Keywords
7AP2 2.25 Å EC: 6.1.1.4 NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH LEUS7HMDDA NEISSERIA GONORRHOEAE PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA SYNTHETASE L
Ref.: SYNTHESIS AND BIOLOGICAL EVALUATION OF 1,3-DIDEAZAPURINE-LIKE 7-AMINO-5-HYDROXYMETHYL-BENZ RIBONUCLEOSIDE ANALOGUES AS AMINOACYL-TRNA SYNTHETA INHIBITORS. MOLECULES V. 25 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:1204;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
EDO A:1202;
A:1201;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
MG A:1205;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
RRW A:1203;
 Valid;
 none;
 submit data
487.527 C19 H29 N5 O8 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: RRW; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 RRW 1 1
2 RUZ 0.852273 0.941176
3 RSN 0.806452 0.930233
4 RRB 0.75 0.930233
5 LSS 0.598039 0.965116
6 SSA 0.5 0.91954
7 5CA 0.490741 0.91954
8 A5A 0.476636 0.906977
9 DSZ 0.468468 0.897727
10 54H 0.46789 0.930233
11 VMS 0.46789 0.930233
12 TSB 0.463636 0.896552
13 GSU 0.45614 0.897727
14 KAA 0.45614 0.888889
15 NVA LMS 0.451327 0.910112
16 53H 0.45045 0.91954
17 YSA 0.449153 0.897727
18 HQ5 0.445455 0.846154
19 52H 0.441441 0.91954
20 WSA 0.432 0.908046
21 L3U 0.419643 0.865169
22 NSS 0.417391 0.897727
23 LSU 0.410714 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: RRW; 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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