Receptor
PDB id Resolution Class Description Source Keywords
3P3E 1.28 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC-009 PSEUDOMONAS AERUGINOSA LIPID A BIOSYNTHESIS LIPID A SYNTHESIS LPXC BAAB SANDWICHHYDROLASE DEACETYLATION ANTIBIOTIC ACYL UDP-GLCNAC HYDRLPC-009
Ref.: SPECIES-SPECIFIC AND INHIBITOR-DEPENDENT CONFORMATI LPXC: IMPLICATIONS FOR ANTIBIOTIC DESIGN. CHEM.BIOL. V. 18 38 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3P3 A:501;
 Valid;
 none;
 submit data
362.379 C21 H18 N2 O4 C[C@H...
NA A:601;
 Invalid;
 none;
 submit data
22.99 Na [Na+]
NO3 A:701;
A:702;
A:703;
A:704;
A:705;
A:706;
A:707;
A:708;
A:709;
A:710;
A:711;
A:712;
A:713;
A:714;
A:715;
A:716;
A:717;
A:718;
A:719;
A:720;
A:721;
A:722;
A:723;
A:724;
A:725;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.005 N O3 [N+](...
ZN A:400;
A:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6MAE 1.8 Å EC: 3.5.1.- CHAIN A. UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DE PA-LPXC COMPLEXED WITH (R)-3-((S)-3-(4-(CYCLOPROPYLETHYNYL)O XOOXAZOLIDIN-5-YL)-N-HYDROXY-2-METHYL-2-(METHYLSULFONYL)PR PSEUDOMONAS AERUGINOSA (STRAIN ATCC 1522644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 /ORGANISM_TAXID: 208964 LPXC HYDROLASE
Ref.: APPLICATION OF VIRTUAL SCREENING TO THE IDENTIFICAT NEW LPXC INHIBITOR CHEMOTYPES, OXAZOLIDINONE AND ISOXAZOLINE. J. MED. CHEM. V. 61 9360 2018
Members (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 7CI4 ic50 = 8.97 uM FXU C12 H15 F3 N2 O4 S CS(=O)(=O)....
3 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
4 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
5 7CI9 ic50 = 20 nM FYL C21 H24 N4 O5 C[C@@H](c1....
6 7CI5 ic50 = 5.69 uM FXX C11 H11 F3 N2 O4 c1cc(cc(c1....
7 6MO5 ic50 = 0.3 nM JWP C22 H26 N2 O7 S CC(C)([C@@....
8 4J3D ic50 = 5.3 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
9 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
10 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
11 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
12 7CIC ic50 = 54.9 uM FZ0 C9 H9 F3 N2 O2 c1cc(cc(c1....
13 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
14 6MO4 ic50 = 4.6 nM JWM C19 H22 N2 O6 S CC(C)([C@@....
15 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
16 7K99 - W4M C23 H27 N5 O3 S CS[C@@H](C....
17 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
18 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
19 3U1Y ic50 < 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
20 7CIB - FYR C13 H10 O3 c1ccc(cc1)....
21 6MOO ic50 = 19 nM A5F C20 H23 N3 O4 CC(C)([C@@....
22 7CIE ic50 = 12.8 uM FZ6 C10 H11 F3 N2 O3 c1cc(cc(c1....
23 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
24 7CID ic50 = 125 uM FZ3 C12 H13 Cl N2 c1cc(ccc1C....
25 7CI7 ic50 = 0.00603 uM FY9 C26 H32 N2 O5 S CS(=O)(=O)....
26 6MAE Kd = 0.065 nM JBA C19 H22 N2 O6 S C[C@@](C[C....
27 7K9A - W8P C23 H22 N6 O3 S CS[C@H](Cn....
28 6MOD ic50 = 0.71 nM JWV C19 H20 N2 O7 S COC1(CS(=O....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 7CI4 ic50 = 8.97 uM FXU C12 H15 F3 N2 O4 S CS(=O)(=O)....
3 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
4 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
5 7CI9 ic50 = 20 nM FYL C21 H24 N4 O5 C[C@@H](c1....
6 7CI5 ic50 = 5.69 uM FXX C11 H11 F3 N2 O4 c1cc(cc(c1....
7 6MO5 ic50 = 0.3 nM JWP C22 H26 N2 O7 S CC(C)([C@@....
8 4J3D ic50 = 5.3 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
9 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
10 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
11 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
12 7CIC ic50 = 54.9 uM FZ0 C9 H9 F3 N2 O2 c1cc(cc(c1....
13 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
14 6MO4 ic50 = 4.6 nM JWM C19 H22 N2 O6 S CC(C)([C@@....
15 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
16 7K99 - W4M C23 H27 N5 O3 S CS[C@@H](C....
17 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
18 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
19 3U1Y ic50 < 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
20 7CIB - FYR C13 H10 O3 c1ccc(cc1)....
21 6MOO ic50 = 19 nM A5F C20 H23 N3 O4 CC(C)([C@@....
22 7CIE ic50 = 12.8 uM FZ6 C10 H11 F3 N2 O3 c1cc(cc(c1....
23 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
24 7CID ic50 = 125 uM FZ3 C12 H13 Cl N2 c1cc(ccc1C....
25 7CI7 ic50 = 0.00603 uM FY9 C26 H32 N2 O5 S CS(=O)(=O)....
26 6MAE Kd = 0.065 nM JBA C19 H22 N2 O6 S C[C@@](C[C....
27 7K9A - W8P C23 H22 N6 O3 S CS[C@H](Cn....
28 6MOD ic50 = 0.71 nM JWV C19 H20 N2 O7 S COC1(CS(=O....
29 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
30 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
31 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
32 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
33 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
34 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
35 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
36 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 7CI4 ic50 = 8.97 uM FXU C12 H15 F3 N2 O4 S CS(=O)(=O)....
3 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
4 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
5 7CI9 ic50 = 20 nM FYL C21 H24 N4 O5 C[C@@H](c1....
6 7CI5 ic50 = 5.69 uM FXX C11 H11 F3 N2 O4 c1cc(cc(c1....
7 6MO5 ic50 = 0.3 nM JWP C22 H26 N2 O7 S CC(C)([C@@....
8 4J3D ic50 = 5.3 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
9 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
10 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
11 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
12 7CIC ic50 = 54.9 uM FZ0 C9 H9 F3 N2 O2 c1cc(cc(c1....
13 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
14 6MO4 ic50 = 4.6 nM JWM C19 H22 N2 O6 S CC(C)([C@@....
15 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
16 7K99 - W4M C23 H27 N5 O3 S CS[C@@H](C....
17 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
18 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
19 3U1Y ic50 < 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
20 7CIB - FYR C13 H10 O3 c1ccc(cc1)....
21 6MOO ic50 = 19 nM A5F C20 H23 N3 O4 CC(C)([C@@....
22 7CIE ic50 = 12.8 uM FZ6 C10 H11 F3 N2 O3 c1cc(cc(c1....
23 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
24 7CID ic50 = 125 uM FZ3 C12 H13 Cl N2 c1cc(ccc1C....
25 7CI7 ic50 = 0.00603 uM FY9 C26 H32 N2 O5 S CS(=O)(=O)....
26 6MAE Kd = 0.065 nM JBA C19 H22 N2 O6 S C[C@@](C[C....
27 7K9A - W8P C23 H22 N6 O3 S CS[C@H](Cn....
28 6MOD ic50 = 0.71 nM JWV C19 H20 N2 O7 S COC1(CS(=O....
29 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
30 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
31 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
32 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
33 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
34 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
35 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
36 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
37 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
38 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
39 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
40 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
41 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
42 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
43 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
44 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
45 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
46 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 3P3; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 3P3 1 1
2 ZH2 0.754098 0.913043
3 5EP 0.557143 0.75
4 L53 0.528571 0.791667
5 ZH4 0.513158 0.791667
6 C90 0.5 0.677419
7 1WM 0.487179 0.854167
8 5EM 0.465753 0.764706
9 5EN 0.435897 0.807692
10 P76 0.421687 0.666667
11 1WN 0.411765 0.84
12 UKW 0.405797 0.818182
13 A5F 0.4 0.678571
14 1JS 0.4 0.696429
15 1WL 0.4 0.644068
Similar Ligands (3D)
Ligand no: 1; Ligand: 3P3; Similar ligands found: 1
No: Ligand Similarity coefficient
1 2CW 0.8832
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6MAE; Ligand: JBA; 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: 6mae.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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