Receptor
PDB id Resolution Class Description Source Keywords
5LSC 1.5 Å EC: 3.5.2.6 THE STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 IN COMPLEX TRIAZOLYLTHIOACETAMIDE INHIBITOR PSEUDOMONAS AERUGINOSA ANTIBIOTIC RESISTANCE CARBAPENEMASES VERONA INTEGRON-ENCODMETALLO-BETA-LACTAMASE 2 VIM-2 HYDROLASE
Ref.: THE STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 I WITH A TRIAZOLYLTHIOACETAMIDE INHIBITOR. ACTA CRYSTALLOGR F STRUCT V. 72 813 2016 BIOL COMMUN
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:406;
B:405;
A:406;
B:407;
A:407;
A:405;
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...
HIS THR ASN ARG B:293;
A:293;
Invalid;
Invalid;
none;
none;
submit data n/a n/a n/a n/a
SER B:297;
A:297;
Invalid;
Invalid;
none;
none;
submit data
105.093 C3 H7 N O3 C([C@...
CL A:402;
A:401;
B:402;
A:403;
B:403;
B:401;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
VAL B:298;
A:298;
Invalid;
Invalid;
none;
none;
submit data
117.146 C5 H11 N O2 CC(C)...
752 A:404;
B:404;
Valid;
Valid;
none;
none;
ic50 = 20 uM
411.458 C18 H13 N5 O3 S2 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FQC 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF THE METALLO-BETA-LACTAMASE VIM-2 WITH 2 PSEUDOMONAS AERUGINOSA HYDROLASE ANTIBIOTIC RESISTANCE
Ref.: STRUCTURAL BASIS OF METALLO-BETA-LACTAMASE, SERINE-BETA-LACTAMASE, AND PENICILLIN BINDING PROTE INHIBITION BY CYCLIC BORONATES NAT.COMMUN. V. 7 12406 2016
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
3 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
4 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
5 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
6 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
7 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
8 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
9 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
10 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
11 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
12 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
13 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
14 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
15 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
3 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
4 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
5 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
6 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
7 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
8 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
9 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
10 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
11 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
12 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
13 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
14 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
15 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
16 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
17 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
18 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
50% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 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 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
5 5NI0 ic50 = 1.89 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
6 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
7 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
8 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
9 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
10 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
11 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
12 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
13 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
14 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
15 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
16 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
17 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
18 1MQO - CIT C6 H8 O7 C(C(=O)O)C....
19 5FQB ic50 = 0.3 uM OK3 C17 H18 B N2 O6 B1([C@H](C....
20 4TYT ic50 = 0.02 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
21 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
22 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
23 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
24 1JJT ic50 = 0.009 uM BDS C20 H18 O8 c1cc2c(cc1....
25 5EV8 - 3R9 C7 H11 N O2 S3 C1[C@@H](N....
26 3WXC - C93 C13 H15 N O5 c1cc(c(c(c....
27 2DOO ic50 = 0.7 uM C4H C19 H27 N3 O3 S2 CN(C)c1ccc....
28 4F6Z - FLC C6 H5 O7 C(C(=O)[O-....
29 1DD6 - MCI C19 H19 N5 O3 S2 c1ccc(cc1)....
30 5EWA Ki = 15 uM 9BZ C9 H15 N O2 S3 CC1([C@H](....
31 1JJE ic50 = 0.0037 uM BYS C19 H18 O6 c1ccc(cc1)....
32 4UAM - FLC C6 H5 O7 C(C(=O)[O-....
33 1M2X Ki ~ 85 uM MCO C9 H15 N O3 S C[C@H](CS)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 752; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 752 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FQC; Ligand: OK3; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 5fqc.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UIU 8CG 0.01511 0.40494 2.89256
2 2BR6 HSL 0.001048 0.42458 3.30579
3 1WRA PC 0.002915 0.43553 3.71901
4 3BIB PSF 0.02551 0.41715 5.17241
5 5HIP 61O 0.002707 0.40213 12.8099
6 4I4S LAT 0.01308 0.40318 13.0137
Pocket No.: 2; Query (leader) PDB : 5FQC; Ligand: OK3; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 5fqc.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3NX2 FER 0.01881 0.40459 3.57143
2 5AIP 4HP 0.02355 0.40454 5.47945
3 4FFG 0U8 0.02055 0.40734 21.0744
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