Receptor
PDB id Resolution Class Description Source Keywords
4J09 1.9 Å EC: 2.3.1.129 CRYSTAL STRUCTURE OF LPXA BOUND TO RJPXD33 ESCHERICHIA COLI ACYLTRANSFERASE LEFT-HANDED BETA HELIX TRANSFERASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION OF PEPTIDE RJP ACYLTRANSFERASES IN LIPID A BIOSYNTHESIS. J.BIOL.CHEM. V. 289 15527 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:301;
A:302;
A:303;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
EDO A:306;
A:305;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
THR ASN LEU TYR MET LEU B:1;
Valid;
none;
submit data
738.928 n/a S(CCC...
DMS A:304;
Invalid;
none;
submit data
78.133 C2 H6 O S CS(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6P9P 2 Å EC: 2.3.1.129 E.COLI LPXA IN COMPLEX WITH COMPOUND 1 ESCHERICHIA COLI ACYLTRANSFERASE TRANSFERASE TRANSFERASE-INHIBITOR COMPLEX
Ref.: TWO DISTINCT MECHANISMS OF INHIBITION OF LPXA ACYLTRANSFERASE ESSENTIAL FOR LIPOPOLYSACCHARIDE BIOSYNTHESIS. J.AM.CHEM.SOC. V. 142 4445 2020
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2QIV - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
2 6P9R ic50 = 3 uM O5M C21 H21 F N4 O2 Cc1ccnc(c1....
3 6P9S ic50 = 11 uM O5G C22 H24 N4 O3 Cc1ccnc(c1....
4 6P9P Kd = 0.1 uM O5J C24 H20 N2 O4 COc1ccc(cc....
5 4J09 - THR ASN LEU TYR MET LEU n/a n/a
6 6P9T ic50 = 0.6 uM O5D C22 H24 Cl N5 O3 Cc1cc(ncc1....
7 2QIA - U20 C31 H53 N3 O19 P2 CCCCCCCCCC....
8 6P9Q Kd = 110 uM O5P C21 H22 N4 O2 Cc1ccnc(c1....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2QIV - U21 C27 H45 N3 O19 P2 CCCCCCC[C@....
2 6P9R ic50 = 3 uM O5M C21 H21 F N4 O2 Cc1ccnc(c1....
3 6P9S ic50 = 11 uM O5G C22 H24 N4 O3 Cc1ccnc(c1....
4 6P9P Kd = 0.1 uM O5J C24 H20 N2 O4 COc1ccc(cc....
5 4J09 - THR ASN LEU TYR MET LEU n/a n/a
6 6P9T ic50 = 0.6 uM O5D C22 H24 Cl N5 O3 Cc1cc(ncc1....
7 2QIA - U20 C31 H53 N3 O19 P2 CCCCCCCCCC....
8 6P9Q Kd = 110 uM O5P C21 H22 N4 O2 Cc1ccnc(c1....
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: THR ASN LEU TYR MET LEU; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 THR ASN LEU TYR MET LEU 1 1
2 THR ASN GLU PHE TYR ALA 0.526786 0.818182
3 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.512397 0.842105
4 ACE GLU ASN LEU TYR PHE GLN SER GLY THR 0.504132 0.789474
5 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.5 0.758065
6 ALA LEU TYR ASN THR ALA ALA ALA LEU 0.495652 0.849057
7 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.488722 0.8
8 FME TYR PHE ILE ASN ILE LEU THR LEU 0.48855 0.928571
9 GLU ASN LEU TYR PHE GLN 0.483051 0.803571
10 GLU LEU ASN ARG LYS MET ILE TYR MET 0.465278 0.769231
11 LYS ALA VAL TYR ASN PHE ALA THR MET 0.465116 0.925926
12 GLU LEU ARG ARG LYS MET MET TYR MET 0.461538 0.75
13 ASP SEP TYR GLU VAL LEU ASP LEU 0.459259 0.741935
14 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.458647 0.821429
15 SER GLN TYR TYR TYR ASN SER LEU 0.452991 0.842105
16 THR PRO TYR ASP ILE ASN GLN MET LEU 0.452055 0.764706
17 ALA VAL TYR ASN PHE ALA THR MET 0.449612 0.927273
18 ALA MET TYR LYS 0.441441 0.789474
19 SER LEU TYR ASN THR VAL ALA THR LEU 0.440945 0.836364
20 ACE GLU LEU LEU MET VAL PRO ASP MET TYR 0.438849 0.716418
21 SER LEU TYR ASN THR ILE ALA THR LEU 0.4375 0.839286
22 SER LEU TYR ASN VAL VAL ALA THR LEU 0.4375 0.836364
23 ALA LEU LYS ILE ASP ASN MET ASP 0.428571 0.758621
24 SER LEU LYS ILE ASP ASN MET ASP 0.426357 0.779661
25 SER LEU PHE ASN THR ILE ALA VAL LEU 0.422222 0.8
26 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.42029 0.842105
27 ASP ALA ASP GLU TYR LEU 0.420168 0.830189
28 PHE TYR ARG ALA LEU MET 0.41791 0.71875
29 TYR LEU ASP SER GLY ILE HIS SER GLY ALA 0.414414 0.781818
30 GLU LEU LYS ARG LYS MET ILE TYR MET 0.412587 0.723077
31 TYR MET PHE PRO ASN ALA PRO TYR LEU 0.412162 0.71831
32 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.411765 0.793103
33 ARG GLN ALA ASN PHE LEU GLY LYS ILE ASN 0.410256 0.709091
34 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.404412 0.859649
35 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.403974 0.738462
36 LYS ALA VAL PHE ASN PHE ALA THR MET 0.403101 0.87037
37 ASP PHE GLU LYS GLU GLY TYR SER LEU 0.401408 0.758065
38 GLY LEU MET TRP LEU SER TYR PHE VAL 0.4 0.769231
39 ILE SER TYR GLY ASN ASP ALA LEU MET PRO 0.4 0.742857
40 GLY ASN TYR SER PHE TYR ALA LEU 0.4 0.779661
Similar Ligands (3D)
Ligand no: 1; Ligand: THR ASN LEU TYR MET LEU; 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 : 6P9P; Ligand: O5J; 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: 6p9p.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6P9P; Ligand: O5J; 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: 6p9p.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6P9P; Ligand: O5J; 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: 6p9p.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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