Receptor
PDB id Resolution Class Description Source Keywords
6Q8A 2.11 Å EC: 6.1.1.4 NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH (L-LEUCYL)-SULFAMOYL)CYTIDINE NEISSERIA GONORRHOEAE (STRAIN NCCP1194ORGANISM_TAXID: 521006 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
HQ5 A:901;
 Valid;
 none;
 submit data
435.453 C15 H25 N5 O8 S CC(C)...
MG A:903;
 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: HQ5; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 HQ5 1 1
2 FZQ 0.802469 0.930233
3 YSC 0.706522 0.91954
4 LSU 0.674157 0.964286
5 L3U 0.648352 0.952941
6 FZK 0.526316 0.895349
7 C 0.523256 0.767442
8 C5P 0.523256 0.767442
9 CAR 0.523256 0.767442
10 FZT 0.515464 0.896552
11 AR3 0.493827 0.686047
12 CTN 0.493827 0.686047
13 CDP 0.48913 0.758621
14 CDP MG 0.48913 0.755814
15 I5A 0.487805 0.674419
16 C2G 0.484848 0.770115
17 HF4 0.473684 0.758621
18 CTP 0.473684 0.758621
19 YSU 0.471698 0.885057
20 Y3U 0.46729 0.886364
21 2TM 0.463918 0.752809
22 CDM 0.461538 0.766667
23 0RC 0.454545 0.764045
24 7XL 0.454545 0.761364
25 LSS 0.45283 0.877778
26 RRW 0.445455 0.846154
27 C5G 0.443396 0.741573
28 OVK 0.441441 0.817204
29 CDC 0.438095 0.771739
30 PMT 0.428571 0.791209
31 A7R 0.426087 0.733333
32 CXY 0.425926 0.761364
33 CDP RB0 0.422018 0.741573
34 1AA 0.421053 0.717391
35 NCC 0.408 0.764045
36 FN5 0.406504 0.731183
37 C5P SIA 0.401575 0.744444
38 V12 0.4 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: HQ5; Similar ligands found: 2
No: Ligand Similarity coefficient
1 UTP 0.8790
2 UDP 0.8747
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
APoc FAQ
Feedback