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
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: R38; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 R59 1 1
2 R38 1 1
3 0ZN 0.552941 0.77551
4 4Z9 0.546875 0.622222
5 3IL 0.546875 0.622222
6 LYS TRP 0.526316 0.714286
7 TRP 0.515152 0.72093
8 DTR 0.515152 0.72093
9 LSW 0.505618 0.745098
10 X95 0.505618 0.745098
11 93W 0.494118 0.616667
12 8NN 0.494118 0.616667
13 GM6 0.488095 0.62069
14 LYS TRP LYS 0.487805 0.705882
15 TRP LEU PHE VAL GLN ARG ASP SER LYS GLU 0.475 0.702128
16 LTN 0.469697 0.681818
17 TYR TRP ALA ALA ALA ALA 0.463158 0.705882
18 IAD 0.453333 0.804348
19 IAV 0.453333 0.804348
20 ACE GLU TRP TRP TRP 0.448276 0.705882
21 ASP TRP ASN 0.447059 0.705882
22 GLU ASP ASN ASP TRP ASN 0.447059 0.705882
23 TR7 0.444444 0.652174
24 ASP ASN ARG LEU GLY LEU VAL TYR TRP PHE 0.4375 0.711538
25 19L 0.436893 0.6
26 TRP GLY 0.434211 0.744681
27 KAW 0.43299 0.679245
28 TYR GLU TRP 0.425532 0.692308
29 MET ASN TRP ASN ILE 0.425532 0.716981
30 IAC 0.424242 0.604651
31 ARG LEU TRP SER 0.42 0.666667
32 TRP GLU GLU LEU 0.417582 0.72549
33 ASP SER TRP LYS ASP GLY CYS TYR 0.4 0.706897
34 RT8 0.4 0.607143
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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