Receptor
PDB id Resolution Class Description Source Keywords
4ISA 1.8 Å EC: 3.5.1.33 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/BB-78485 COMP ESCHERICHIA COLI LIPID A SYNTHESIS LPXC BAAB SANDWICH DEACETYLATION ANTIBACYL UDP-GLCNAC HYDROXAMATE BB-78485 HYDROLASE-HYDROLASEINHIBITOR 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
FMT A:404;
A:411;
A:419;
A:406;
A:415;
A:417;
A:409;
A:410;
A:418;
A:413;
A:414;
A:420;
A:416;
A:407;
A:405;
A:412;
A:408;
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;
submit data
46.025 C H2 O2 C(=O)...
D1D A:421;
Invalid;
none;
submit data
152.235 C4 H8 O2 S2 C1[C@...
GVR A:403;
A:402;
Valid;
Valid;
none;
none;
submit data
420.481 C23 H20 N2 O4 S c1ccc...
ZN A:401;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
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 2 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 (26)
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 6MO5 ic50 = 0.3 nM JWP C22 H26 N2 O7 S CC(C)([C@@....
5 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
6 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
7 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
8 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
9 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
10 6MO4 ic50 = 4.6 nM JWM C19 H22 N2 O6 S CC(C)([C@@....
11 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
12 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
13 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
14 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
15 6MOO ic50 = 19 nM A5F C20 H23 N3 O4 CC(C)([C@@....
16 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
17 6MAE Kd = 0.065 nM JBA C19 H22 N2 O6 S C[C@@](C[C....
18 6MOD ic50 = 0.71 nM JWV C19 H20 N2 O7 S COC1(CS(=O....
19 3NZK Ki = 0.54 nM C90 C24 H27 N3 O5 C[C@H]([C@....
20 4MQY - UKW C13 H12 N2 O4 C[C@H]([C@....
21 4IS9 - LTF C15 H20 N2 O5 CCCc1cc(cc....
22 3PS1 - UKW C13 H12 N2 O4 C[C@H]([C@....
23 4ISA - GVR C23 H20 N2 O4 S c1ccc2cc(c....
24 3P3G Ki = 0.18 nM 3P3 C21 H18 N2 O4 C[C@H]([C@....
25 3PS2 - UKW C13 H12 N2 O4 C[C@H]([C@....
26 3PS3 - L53 C21 H17 N3 O4 C[C@@H]([C....
50% Homology Family (36)
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 6MO5 ic50 = 0.3 nM JWP C22 H26 N2 O7 S CC(C)([C@@....
5 4J3D ic50 = 4.4 nM 1JS C23 H25 N3 O5 c1ccc(cc1)....
6 2VES - GVR C23 H20 N2 O4 S c1ccc2cc(c....
7 5DRR - 5EN C22 H19 F2 N3 O4 C[C@]([C@@....
8 4LCG - 1WM C26 H21 N3 O5 c1cc(ccc1C....
9 3P3E - 3P3 C21 H18 N2 O4 C[C@H]([C@....
10 6MO4 ic50 = 4.6 nM JWM C19 H22 N2 O6 S CC(C)([C@@....
11 5N8C - 8Q8 C27 H31 N5 O3 CC(C)([C@@....
12 5DRQ - 5EM C22 H22 N4 O3 CC(C)([C@@....
13 5U39 - C90 C24 H27 N3 O5 C[C@H]([C@....
14 3U1Y ic50 = 2.13 nM 03I C25 H34 N2 O6 S C[C@@](CCc....
15 6MOO ic50 = 19 nM A5F C20 H23 N3 O4 CC(C)([C@@....
16 4LCF - 1WL C23 H19 N5 O3 c1cc(ccc1C....
17 6MAE Kd = 0.065 nM JBA C19 H22 N2 O6 S C[C@@](C[C....
18 6MOD ic50 = 0.71 nM JWV C19 H20 N2 O7 S COC1(CS(=O....
19 5DRP - 5EP C23 H23 N3 O3 CC[C@H](C)....
20 4U3D - 3BX C26 H30 N2 O5 c1cc(ccc1C....
21 5U86 - 81V C25 H27 F2 N3 O5 C[C@]([C@@....
22 4U3B - 3BW C19 H20 Cl N O4 S c1cc(ccc1O....
23 5DRO - ZH2 C21 H19 N3 O4 C[C@H]([C@....
24 2J65 - MYR C14 H28 O2 CCCCCCCCCC....
25 3P3C - 3P3 C21 H18 N2 O4 C[C@H]([C@....
26 1P42 - MYR C14 H28 O2 CCCCCCCCCC....
27 3P76 - P76 C24 H27 N3 O4 C[C@H]([C@....
28 2O3Z Kd = 2 uM AI7 C14 H20 O3 CCCCCCCOc1....
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....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GVR; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GVR 1 1
2 FD4 0.43617 0.614458
3 FD3 0.421053 0.62963
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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