Receptor
PDB id Resolution Class Description Source Keywords
5DRQ 1.63 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC-040 PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15PAO1 / 1C / PRS 101 / LMG 12228) LPXC LIPID A INHIBITOR GRAM-NEGATIVE BACTERIA HYDROLASE-INHIBITOR COMPLEX
Ref.: DRUG DESIGN FROM THE CRYPTIC INHIBITOR ENVELOPE. NAT COMMUN V. 7 10638 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NO3 A:331;
A:325;
A:304;
A:318;
A:306;
A:308;
A:330;
A:320;
A:313;
A:307;
A:332;
A:324;
A:327;
A:312;
A:326;
A:316;
A:305;
A:323;
A:319;
A:309;
A:321;
A:329;
A:328;
A:314;
A:310;
A:322;
A:315;
A:311;
A:317;
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;
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;
none;
none;
none;
none;
submit data
62.005 N O3 [N+](...
5EM A:303;
Valid;
none;
submit data
390.435 C22 H22 N4 O3 CC(C)...
ZN A:302;
A:301;
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
5U3B 2 Å EC: 3.5.1.- PSEUDOMONAS AERUGINOSA LPXC IN COMPLEX WITH NVS-LPXC-01 PSEUDOMONAS AERUGINOSA (STRAIN ATCC 1522644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 /ORGANISM_TAXID: 208964 LPXC HYDROXYMATE GRAM NEGATIVE HYDROLASE
Ref.: DESIGN, SYNTHESIS, AND PROPERTIES OF A POTENT INHIB PSEUDOMONAS AERUGINOSA DEACETYLASE LPXC. J. MED. CHEM. V. 60 5002 2017
Members (13)
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 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
14 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
15 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
16 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
17 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
18 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
19 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
20 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
21 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3UHM ic50 = 3.6 nM RFN C17 H20 N2 O5 S C[C@@](CCN....
2 4LCH - 1WN C27 H23 N3 O5 C[C@](c1cc....
3 5U3B ic50 = 1.5 nM 7TD C16 H21 N3 O4 CC#CCOc1cc....
4 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
5 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
6 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
7 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
8 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
9 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
10 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
11 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
12 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
13 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
14 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
15 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
16 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
17 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
18 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
19 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
20 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
21 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
22 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
23 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
24 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
25 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
26 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
27 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
28 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
29 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
30 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
31 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5EM; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 5EM 1 1
2 5EN 0.734375 0.818182
3 1WN 0.652778 0.849057
4 ZH2 0.630769 0.843137
5 5EP 0.61194 0.830189
6 L53 0.536232 0.735849
7 1WM 0.533333 0.792453
8 7TD 0.528571 0.77193
9 2CW 0.521127 0.811321
10 1WL 0.512821 0.716667
11 3P3 0.465753 0.764706
12 ZH4 0.407407 0.735849
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5U3B; Ligand: 7TD; 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: 5u3b.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5U3B; Ligand: 7TD; 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: 5u3b.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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