Receptor
PDB id Resolution Class Description Source Keywords
4MQY 2.01 Å EC: 3.5.1.33 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/LPC-138 COMPL ESCHERICHIA COLI LPXC ANTIBIOTIC ACYL UDP-GLCNAC HYDROXAMATE LPC-138 BAASANDWICH LIPID A BIOSYNTHESIS LIPID A SYNTHESIS DEACETYLHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS OF THE PROMISCUOUS INHIBITOR SUSCE OF ESCHERICHIA COLI LPXC. ACS CHEM.BIOL. V. 9 237 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:405;
A:408;
A:406;
A:407;
A:404;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
DMS A:403;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
UKW A:409;
 Valid;
 none;
 submit data
260.245 C13 H12 N2 O4 C[C@H...
ZN A:401;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
2CW A:402;
 Valid;
 none;
 submit data
389.404 C22 H19 N3 O4 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NZK 1.8 Å EC: 3.5.1.33 STRUCTURE OF LPXC FROM YERSINIA ENTEROCOLITICA COMPLEXED WIT INHIBITOR YERSINIA ENTEROCOLITICA DEACETYLASE ENDOTOXIN METAL-BINDING HYDROLASE
Ref.: STRUCTURE OF THE METAL-DEPENDENT DEACETYLASE LPXC F YERSINIA ENTEROCOLITICA COMPLEXED WITH THE POTENT I CHIR-090 . BIOCHEMISTRY V. 50 258 2010
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
2 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
3 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
4 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
5 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
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: UKW; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 UKW 1 1
2 L53 0.627119 0.863636
3 ZH4 0.552239 0.863636
4 ZH2 0.411765 0.75
5 3P3 0.405797 0.818182
Ligand no: 2; Ligand: 2CW; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 2CW 1 1
2 L53 0.565217 0.916667
3 5EM 0.521127 0.811321
4 ZH2 0.5 0.843137
5 5EP 0.486486 0.732143
6 5EN 0.467532 0.818182
7 ZH4 0.45 0.916667
8 1WN 0.423529 0.849057
9 1WM 0.409639 0.792453
Similar Ligands (3D)
Ligand no: 1; Ligand: UKW; Similar ligands found: 16
No: Ligand Similarity coefficient
1 147 0.8954
2 GAL PHB 0.8790
3 IM4 0.8753
4 TH4 0.8727
5 KHP 0.8725
6 BNY 0.8718
7 7ZO 0.8696
8 CMG 0.8671
9 4K2 0.8633
10 JVD 0.8624
11 NPX 0.8622
12 JNW 0.8619
13 IEE 0.8613
14 GAL NPO 0.8608
15 56N 0.8604
16 CT7 0.8588
Ligand no: 2; Ligand: 2CW; Similar ligands found: 1
No: Ligand Similarity coefficient
1 3P3 0.8832
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NZK; Ligand: C90; 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: 3nzk.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3NZK; Ligand: C90; 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: 3nzk.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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