Receptor
PDB id Resolution Class Description Source Keywords
5N4S 1.2 Å EC: 3.5.2.6 VIM-2 METALLO-BETA-LACTAMASE IN COMPLEX WITH ((S)-3-MERCAPTO METHYLPROPANOYL)-D-TRYPTOPHAN (COMPOUND 3) PSEUDOMONAS AERUGINOSA METALLO-BETA-LACTAMASE INHIBITOR COMPLEX ANTIBIOTIC RESISHYDROLASE
Ref.: CRYSTALLOGRAPHIC ANALYSES OF ISOQUINOLINE COMPLEXES NEW MODE OF METALLO-BETA-LACTAMASE INHIBITION. CHEM. COMMUN. (CAMB.) V. 53 5806 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:502;
B:503;
A:501;
A:503;
B:502;
B:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
R38 A:504;
B:504;
Valid;
Valid;
none;
none;
ic50 = 0.055 uM
306.38 C15 H18 N2 O3 S C[C@H...
FMT B:505;
A:505;
B:506;
A:506;
B:508;
B:507;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6EW3 2.14 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH M PSEUDOMONAS AERUGINOSA METAL BINDING HYDROLASE ANTIBIOTIC RESISTANCE XCHEM COMP
Ref.: STRUCTURE ACTIVITY RELATIONSHIP STUDIES ON RHODANIN DERIVED ENETHIOL INHIBITORS OF METALLO-BETA-LACTAMA BIOORG. MED. CHEM. V. 26 2928 2018
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
3 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
4 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
5 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
6 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
7 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
8 6EW3 ic50 = 0.04 nM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
9 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
10 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
11 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
12 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
13 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
14 5MXR ic50 = 1.9 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
15 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
16 5MXQ ic50 = 6.2 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
17 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
18 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
19 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
20 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
21 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
3 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
4 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
5 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
6 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
7 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
8 6EW3 ic50 = 0.04 nM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
9 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
10 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
11 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
12 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
13 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
14 5MXR ic50 = 1.9 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
15 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
16 5MXQ ic50 = 6.2 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
17 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
18 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
19 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
20 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
21 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
22 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
23 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
24 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
50% Homology Family (55)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 1HLK Ki = 10 uM 113 C15 H14 O8 C[C@H]1CC2....
2 1KR3 Ki = 10 uM 113 C15 H14 O8 C[C@H]1CC2....
3 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
4 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
5 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
6 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
7 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
8 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
9 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
10 6EW3 ic50 = 0.04 nM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
11 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
12 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
13 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
14 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
15 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
16 5MXR ic50 = 1.9 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
17 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
18 5MXQ ic50 = 6.2 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
19 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
20 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
21 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
22 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
23 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
24 6EUM ic50 = 0.3 uM BY5 C9 H5 F3 O2 S c1cc(c(c(c....
25 6EWE ic50 = 3.1 uM C0W C11 H8 O2 S2 c1ccc2c(c1....
26 6F2N ic50 = 0.2 uM CF8 C20 H16 O2 S c1ccc2cc(c....
27 1MQO - CIT C6 H8 O7 C(C(=O)O)C....
28 5FQB ic50 = 0.3 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
29 4TYT ic50 = 0.02 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
30 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
31 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
32 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
33 5NDB - 8TW C7 H8 Cl2 O4 S C1=S[C@H]2....
34 5YPI - 8YF C12 H19 N3 O5 S [H]/N=C/NC....
35 5ZGE - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
36 5ZGR - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
37 5YPM - 8YL C17 H27 N3 O6 S C[C@@H]1[C....
38 5ZGQ - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
39 4EY2 - 0RM C17 H22 N2 O7 S CC1([C@@H]....
40 5YPL - HIW C12 H19 N3 O5 S [H]/N=CNCC....
41 5ZGP - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
42 5ZGI - SIN C4 H6 O4 C(CC(=O)O)....
43 1JJT ic50 = 0.009 uM BDS C20 H18 O8 c1cc2c(cc1....
44 5EV8 - 3R9 C7 H11 N O2 S3 C1[C@@H](N....
45 3WXC - C93 C13 H15 N O5 c1cc(c(c(c....
46 2DOO ic50 = 0.7 uM C4H C19 H27 N3 O3 S2 CN(C)c1ccc....
47 4F6Z - FLC C6 H5 O7 C(C(=O)[O-....
48 1DD6 - MCI C19 H19 N5 O3 S2 c1ccc(cc1)....
49 5EWA Ki = 15 uM 9BZ C9 H15 N O2 S3 CC1([C@H](....
50 1JJE ic50 = 0.0037 uM BYS C19 H18 O6 c1ccc(cc1)....
51 4UAM - FLC C6 H5 O7 C(C(=O)[O-....
52 4EYF - PNK C16 H20 N2 O5 S CC1([C@@H]....
53 4EYB - 0WO C19 H21 N3 O6 S Cc1c(c(no1....
54 4EYL - 0RV C17 H25 N3 O6 S CC1=C(C(=N....
55 1M2X Ki ~ 85 uM MCO C9 H15 N O3 S C[C@H](CS)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: R38; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 R38 1 1
2 R59 1 1
3 0ZN 0.552941 0.77551
4 4Z9 0.546875 0.622222
5 3IL 0.546875 0.622222
6 DTR 0.515152 0.72093
7 TRP 0.515152 0.72093
8 X95 0.505618 0.745098
9 LSW 0.505618 0.745098
10 8NN 0.494118 0.616667
11 93W 0.494118 0.616667
12 GM6 0.488095 0.62069
13 LTN 0.469697 0.681818
14 LYS TRP 0.463415 0.74
15 TYR TRP ALA ALA ALA ALA 0.463158 0.692308
16 IAD 0.453333 0.804348
17 IAV 0.453333 0.804348
18 ACE GLU TRP TRP TRP 0.448276 0.705882
19 TRP GLY 0.447368 0.770833
20 TR7 0.444444 0.652174
21 19L 0.436893 0.6
22 GLU ASP ASN ASP TRP ASN 0.436782 0.705882
23 ASP TRP ASN 0.436782 0.705882
24 KAW 0.43299 0.679245
25 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.428571 0.698113
26 TYR GLU TRP 0.425532 0.679245
27 IAC 0.424242 0.604651
28 LYS TRP LYS 0.422222 0.711538
29 MET ASN TRP ASN ILE 0.421053 0.716981
30 TRP GLU GLU LEU 0.413043 0.711538
31 TRP LEU PHE VAL GLN ARG ASP SER LYS GLU 0.408602 0.7
32 VSK 0.406977 0.611111
33 ARG LEU TRP SER 0.403846 0.666667
34 RT8 0.4 0.607143
35 PCA ASN TRP 0.4 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6EW3; Ligand: S3C; 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: 6ew3.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6EW3; Ligand: S3C; 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: 6ew3.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback