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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 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: 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 with APoc: 29
This union binding pocket(no: 1) in the query (biounit: 3nzk.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5TVI MYR None
2 4XCP PLM 2.35294
3 3HQ9 OXL 2.89389
4 3BOF HCS 2.89389
5 1Q8A HCS 2.89389
6 4WGF HX2 2.92683
7 6BJO DUY 3.2
8 5LX9 OLB 3.87324
9 4JLS 3ZE 4.60526
10 2HYR BGC GLC 4.91803
11 2NUO BGC 4.91803
12 2GUD MAN 4.91803
13 2GUD BMA 4.91803
14 2GUC MAN 4.91803
15 2HYQ MAN MAN 4.91803
16 2NU5 NAG 4.91803
17 5M90 JIF 5.14469
18 2CYB TYR 5.14469
19 5MRH Q9Z 6.10932
20 2VDF OCT 6.71937
21 2CYC TYR 6.75241
22 1MJT NAD 7.71704
23 5YRI GLC GLC 13.3803
24 5YRL GLC GLC 13.3803
25 5YRM BGC GLC 13.3803
26 5YRG BGC GLC 13.3803
27 5YRJ BGC GLC 13.3803
28 5YRF GLC GLC 13.3803
29 3VY6 BGC BGC 17.0213
Pocket No.: 2; Query (leader) PDB : 3NZK; Ligand: C90; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 3nzk.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4CP8 MLI 2.2508
2 6CAM BGC 2.2508
3 5EW9 5VC 3.32103
4 4L9Z COA 3.53698
5 4L9Z OXL 3.53698
6 6C6O ENG 4.18006
7 4JZB P2H 4.50161
8 4K10 NI9 4.50161
9 1C3M MAN MAN 4.7619
10 2VAR AMP 5.46624
11 2J5B TYE 6.10932
12 1B4P GPS 6.91244
13 3LGS ADE 7.11611
14 4ZJS 4P0 7.3913
15 1XXR MAN 8.69565
16 3O5N BR0 8.92857
17 4YSX FAD 9.61539
18 3UBQ SIA GAL 12.9944
19 1HBK MYR 15.7303
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