Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C90 A:501;
B:501;
Valid;
Valid;
none;
none;
Ki = 0.54 nM
437.488 C24 H27 N3 O5 C[C@H...
GOL A:3968;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
ZN A:307;
B:307;
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
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 (1)
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@....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 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: C90; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 C90 1 1
2 81V 0.662651 0.911765
3 ZH2 0.506329 0.636364
4 3P3 0.5 0.677419
5 3BX 0.451613 0.814286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NZK; Ligand: C90; Similar sites found: 10
This union binding pocket(no: 1) in the query (biounit: 3nzk.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Q8A HCS 0.02346 0.40302 2.89389
2 2NUO BGC 0.01152 0.43432 4.91803
3 2GUC MAN 0.01153 0.43103 4.91803
4 2NU5 NAG 0.01206 0.42819 4.91803
5 2CYB TYR 0.01914 0.40688 5.14469
6 5MRH Q9Z 0.0178 0.40378 6.10932
7 2VDF OCT 0.02182 0.42733 6.71937
8 2CYC TYR 0.0094 0.42428 6.75241
9 5MX4 HPA 0.006638 0.43295 8.58369
10 3VY6 BGC BGC 0.002957 0.4657 17.0213
Pocket No.: 2; Query (leader) PDB : 3NZK; Ligand: C90; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 3nzk.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L9Z COA 0.0128 0.4051 3.53698
2 4L9Z OXL 0.01313 0.40338 3.53698
3 2J5B TYE 0.02193 0.40422 6.10932
4 4YSX FAD 0.02362 0.40211 9.61539
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