Receptor
PDB id Resolution Class Description Source Keywords
5DEP 2.16 Å EC: 2.3.1.129 STRUCTURE OF PSEUDOMONAS AERUGINOSA LPXA IN COMPLEX WITH UDP PSEUDOMONAS AERUGINOSA (STRAIN PA7) ACYLTRANSFERASE CATALYTIC DOMAIN FATTY ACIDS LIPID A SUBSSPECIFICITY URIDINE DIPHOSPHATE N-ACETYLGLUCOSAMINE HYDRORULERS TRANSFERASE
Ref.: STRUCTURES OF PSEUDOMONAS AERUGINOSA LPXA REVEAL TH FOR ITS SUBSTRATE SELECTIVITY. BIOCHEMISTRY V. 54 5937 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UD1 F:301;
D:302;
E:302;
F:302;
B:302;
B:303;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
 submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
PO4 D:301;
E:301;
B:304;
B:301;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6UEG 2 Å EC: 2.3.1.129 PSEUDOMONAS AERUGINOSA LPXA COMPLEX STRUCTURE WITH LIGAND PSEUDOMONAS AERUGINOSA (STRAIN PA7) LPXA LIGAND COMPLEX TRIMER ACYL TRANSFERASE TRANSFERASE
Ref.: DISCOVERY OF DUAL-ACTIVITY SMALL-MOLECULE LIGANDS O PSEUDOMONAS AERUGINOSA LPXA AND LPXD USING SPR AND CRYSTALLOGRAPHY. SCI REP V. 9 15450 2019
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6UEE - Q5M C14 H12 O3 c1ccc2c(c1....
2 6UEG Kd = 19.5 uM Q5G C14 H16 N2 O5 S c1ccc2c(c1....
3 5DG3 - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
4 5DEP - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6UEE - Q5M C14 H12 O3 c1ccc2c(c1....
2 6UEG Kd = 19.5 uM Q5G C14 H16 N2 O5 S c1ccc2c(c1....
3 5DG3 - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
4 5DEP - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3I3X - U22 C29 H50 N4 O18 P2 CCCCCCCCC[....
2 3I3A - S2N C24 H47 N2 O9 P S CCCCCCCCC[....
3 2QIV - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
4 6P9R ic50 = 3 uM O5M C21 H21 F N4 O2 Cc1ccnc(c1....
5 6P9S ic50 = 11 uM O5G C22 H24 N4 O3 Cc1ccnc(c1....
6 6P9P Kd = 0.1 uM O5J C24 H20 N2 O4 COc1ccc(cc....
7 4J09 - THR ASN LEU TYR MET LEU n/a n/a
8 6P9T ic50 = 0.6 uM O5D C22 H24 Cl N5 O3 Cc1cc(ncc1....
9 2QIA - U20 C31 H53 N3 O19 P2 CCCCCCCCCC....
10 6P9Q Kd = 110 uM O5P C21 H22 N4 O2 Cc1ccnc(c1....
11 4R37 - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
12 1J2Z - SOG C14 H28 O5 S CCCCCCCCS[....
13 6UEE - Q5M C14 H12 O3 c1ccc2c(c1....
14 6UEG Kd = 19.5 uM Q5G C14 H16 N2 O5 S c1ccc2c(c1....
15 5DG3 - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
16 5DEP - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EEB 0.742857 0.971429
7 EPU 0.742857 0.971429
8 F5P 0.742574 0.957143
9 F5G 0.742574 0.971014
10 UD4 0.742574 0.957143
11 UPG 0.73913 0.985294
12 GDU 0.73913 0.985294
13 UFM 0.73913 0.985294
14 UD7 0.722772 0.971014
15 MJZ 0.715686 0.957143
16 UPF 0.697917 0.930556
17 U2F 0.697917 0.930556
18 UMA 0.690265 0.985507
19 UDM 0.683168 0.957143
20 UFG 0.663265 0.930556
21 HWU 0.660377 0.943662
22 12V 0.660377 0.943662
23 AWU 0.659794 0.985294
24 U20 0.655462 0.871795
25 U21 0.655462 0.871795
26 U22 0.655462 0.85
27 UGA 0.65 0.970588
28 UGB 0.65 0.970588
29 USQ 0.633663 0.835443
30 UAD 0.63 0.956522
31 UDX 0.63 0.956522
32 UGF 0.627451 0.916667
33 UDP 0.622222 0.927536
34 UTP 0.619565 0.927536
35 UAG 0.617188 0.931507
36 U5F 0.612903 0.927536
37 URM 0.6 0.942857
38 660 0.6 0.942857
39 G3N 0.596154 0.929577
40 UPU 0.587629 0.955882
41 4RA 0.584615 0.87013
42 UNP 0.583333 0.901408
43 3UC 0.575472 0.930556
44 UML 0.564286 0.871795
45 IUG 0.561404 0.825
46 U5P 0.555556 0.913043
47 U 0.555556 0.913043
48 UDP GAL 0.552381 0.956522
49 UD0 0.552239 0.858974
50 UPP 0.543689 0.928571
51 UDH 0.543689 0.855263
52 2KH 0.530612 0.901408
53 44P 0.521277 0.888889
54 C5G 0.518519 0.930556
55 UDP UDP 0.505155 0.898551
56 Y6W 0.504673 0.90411
57 2QR 0.485075 0.860759
58 2GW 0.482759 0.943662
59 URI 0.477273 0.852941
60 UP5 0.47541 0.844156
61 PMP UD1 0.467626 0.848101
62 1GW 0.467213 0.905405
63 CJB 0.461538 0.838235
64 UAG API 0.457516 0.87013
65 4TC 0.456 0.822785
66 CSQ 0.452991 0.866667
67 CSV 0.452991 0.866667
68 U3P 0.447917 0.898551
69 UA3 0.447917 0.898551
70 GN1 0.444444 0.753623
71 NG1 0.444444 0.753623
72 C30 0.433628 0.696203
73 Q5S 0.433628 0.696203
74 FZK 0.431193 0.771084
75 PUP 0.429825 0.875
76 LSU 0.428571 0.732558
77 CXY 0.422414 0.90411
78 U2P 0.418367 0.913043
79 UMA FGA LYS DAL DAL 0.414634 0.8375
80 U1S 0.409091 0.789474
81 FN5 0.40458 0.883117
82 YSU 0.403361 0.741176
83 DAU 0.403361 0.905405
Similar Ligands (3D)
Ligand no: 1; Ligand: UD1; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GDD 0.8671
2 TDX 0.8645
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6UEG; Ligand: Q5G; 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: 6ueg.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6UEG; Ligand: Q5G; 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: 6ueg.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6UEG; Ligand: Q5G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6ueg.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6UEG; Ligand: Q5G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6ueg.bio2) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6UEG; Ligand: Q5G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6ueg.bio2) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6UEG; Ligand: Q5G; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 6ueg.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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