Receptor
PDB id Resolution Class Description Source Keywords
2YZ3 2.3 Å EC: 3.5.2.6 CRYSTALLOGRAPHIC INVESTIGATION OF INHIBITION MODE OF THE VIM-2 METALLO-BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA W ITH MERCAPTOCARBOXYLATE INHIBITOR PSEUDOMONAS PUTIDA METALLO-BETA-LACTAMASE ENZYME-INHIBITOR COMPLEX HYDROLASE
Ref.: CRYSTALLOGRAPHIC INVESTIGATION OF THE INHIBITION MODE OF A VIM-2 METALLO-BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA BY A MERCAPTOCARBOXYLATE INHIBITOR. J.MED.CHEM. V. 50 6647 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
M5P A:401;
B:402;
 Valid;
Valid;
 none;
none;
 Ki = 220 nM
224.319 C12 H16 O2 S c1ccc...
SO4 A:502;
A:503;
B:501;
B:504;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
ZN A:301;
A:302;
B:303;
B:304;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
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 PROTEI INHIBITION BY CYCLIC BORONATES. NAT COMMUN V. 7 12406 2016
Members (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 48 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 6DD0 Ki = 3.3 uM P9T C10 H7 F2 O5 P c1c(cc(c2c....
3 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
4 6RPN ic50 = 0.2 uM KDZ C16 H16 B O5 S [B-]1([C@H....
5 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 [B-]1([C@H....
6 6TM9 ic50 = 0.23 uM 9NW C16 H21 Cl2 N5 O2 S c1cc(c(cc1....
7 5NI0 ic50 = 1.8 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
8 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
9 6JN6 Ki = 0.07 uM BY0 C14 H18 B N O4 S B([C@@H](C....
10 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
11 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
12 6EW3 ic50 = 0.04 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
13 6O5T Ki = 0.316 uM L8J C10 H8 Br2 N O4 P c1c(cc(c2c....
14 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
15 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
16 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
17 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
18 6TGI Ki = 41 uM N8Z C9 H12 Cl N5 S CCn1c(nnc1....
19 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
20 5MXR ic50 = 6.2 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
21 6SP7 ic50 = 0.026 uM K9B C19 H29 B N3 O6 [B-]1([C@H....
22 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
23 5MXQ ic50 = 1.9 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
24 6J8R Ki = 0.76 uM BHU C5 H12 B N O3 S B(CNC(=O)[....
25 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
26 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
27 6YRP Kd = 389 nM PJB C17 H16 N4 O4 S COc1ccc(c(....
28 6DD1 Ki = 22.3 uM M3Q C10 H10 N O3 P c1cc2cccnc....
29 6ZGM - QKK C12 H11 F2 N7 O5 S2 [H]/N=C(N)....
30 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
31 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
32 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
33 6V1P - QNA C10 H9 B F O5 [B-]1([C@@....
70% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
2 6DD0 Ki = 3.3 uM P9T C10 H7 F2 O5 P c1c(cc(c2c....
3 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
4 6RPN ic50 = 0.2 uM KDZ C16 H16 B O5 S [B-]1([C@H....
5 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 [B-]1([C@H....
6 6TM9 ic50 = 0.23 uM 9NW C16 H21 Cl2 N5 O2 S c1cc(c(cc1....
7 5NI0 ic50 = 1.8 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
8 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
9 6JN6 Ki = 0.07 uM BY0 C14 H18 B N O4 S B([C@@H](C....
10 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
11 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
12 6EW3 ic50 = 0.04 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
13 6O5T Ki = 0.316 uM L8J C10 H8 Br2 N O4 P c1c(cc(c2c....
14 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
15 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
16 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
17 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
18 6TGI Ki = 41 uM N8Z C9 H12 Cl N5 S CCn1c(nnc1....
19 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
20 5MXR ic50 = 6.2 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
21 6SP7 ic50 = 0.026 uM K9B C19 H29 B N3 O6 [B-]1([C@H....
22 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
23 5MXQ ic50 = 1.9 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
24 6J8R Ki = 0.76 uM BHU C5 H12 B N O3 S B(CNC(=O)[....
25 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
26 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
27 6YRP Kd = 389 nM PJB C17 H16 N4 O4 S COc1ccc(c(....
28 6DD1 Ki = 22.3 uM M3Q C10 H10 N O3 P c1cc2cccnc....
29 6ZGM - QKK C12 H11 F2 N7 O5 S2 [H]/N=C(N)....
30 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
31 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
32 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
33 6V1P - QNA C10 H9 B F O5 [B-]1([C@@....
34 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
35 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
36 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
37 6TMC ic50 = 0.53 uM NL5 C14 H19 N3 O3 S CC(C)OCc1c....
50% Homology Family (108)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 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 6D1H Ki = 190.2 uM KED C10 H10 N O4 P c1ccc2c(c1....
4 6V1M - QNA C10 H9 B F O5 [B-]1([C@@....
5 6OVZ - N9M C9 H9 N O5 c1ccc(cc1)....
6 6D1B Ki = 123.7 uM FUJ C11 H11 O6 P COc1ccc2c(....
7 6LJ6 ic50 = 11.1 uM EFF C10 H18 N2 O2 S C[C@H](CS)....
8 6LJ8 ic50 = 19.8 uM EG0 C11 H19 N O3 S C[C@H](CS)....
9 4RL0 - 3S0 C16 H18 N4 O9 S CO/N=C(/c1....
10 5O2E - 3S0 C16 H18 N4 O9 S CO/N=C(/c1....
11 5YPN - LMP C17 H27 N3 O6 S C[C@H]1[C@....
12 6NY7 - L8J C10 H8 Br2 N O4 P c1c(cc(c2c....
13 6LJ0 ic50 = 6.9 uM EER C10 H17 N O3 S C[C@H](CS)....
14 5YPK - HIW C12 H19 N3 O5 S [H]/N=CNCC....
15 5O2F - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
16 6D1E - XJE C12 H13 O6 P Cc1cc2c(c(....
17 6D1D Ki = 33.8 uM GTV C12 H13 O5 P Cc1cc(c2c(....
18 4RL2 - 3S3 C16 H20 N3 O5 S C[C@@H]1CS....
19 6RMF - K9B C19 H29 B N3 O6 [B-]1([C@H....
20 6EFJ Ki = 477 uM O5E C15 H14 N6 O c1ccc(cc1)....
21 6D1I Ki = 81 uM T6Z C11 H12 N O4 P CN1c2ccccc....
22 5YPI - 8YF C12 H19 N3 O5 S [H]/N=C/NC....
23 5ZGE - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
24 6LJ5 ic50 = 4.9 uM EF0 C10 H17 N O3 S C[C@H](CS)....
25 5ZGR - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
26 6LJ2 ic50 = 4.6 uM EKX C14 H17 N O3 S C[C@H](CS)....
27 6MDU Ki = 56 uM N1G C17 H13 N7 O c1ccc(cc1)....
28 5YPM - 8YL C17 H27 N3 O6 S C[C@@H]1[C....
29 4EYF - PNK C16 H20 N2 O5 S CC1([C@@H]....
30 4EYB - 0WO C19 H21 N3 O6 S Cc1c(c(no1....
31 5ZGQ - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
32 6D1F - P9T C10 H7 F2 O5 P c1c(cc(c2c....
33 6O3R - XJE C12 H13 O6 P Cc1cc2c(c(....
34 6LIZ ic50 = 20.4 uM EEO C11 H19 N O3 S C[C@H](CS)....
35 6LIP ic50 = 75 uM EEL C9 H15 N O3 S2 C1C[C@@H](....
36 6D1A Ki = 44.3 uM TWB C12 H13 O5 P Cc1cc2c(cc....
37 4EYL - 0RV C17 H25 N3 O6 S CC1=C(C(=N....
38 6LJ7 ic50 = 27.9 uM EFR C11 H20 N2 O2 S C[C@H](CS)....
39 6D1K Ki = 741.3 uM M3Q C10 H10 N O3 P c1cc2cccnc....
40 4EY2 - 0RM C17 H22 N2 O7 S CC1([C@@H]....
41 6D1J Ki = 56.2 uM 7SX C12 H14 N O4 P Cc1cc(c2c(....
42 6TGD - N8Q C12 H14 N4 O S c1cc(cnc1)....
43 6LJ4 ic50 = 28.4 uM EF9 C10 H17 N O3 S C[C@H](CS)....
44 6OL8 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
45 5YPL - HIW C12 H19 N3 O5 S [H]/N=CNCC....
46 6LJ1 ic50 = 4.6 uM EEX C14 H17 N O3 S C[C@H](CS)....
47 6D1C - VKE C11 H9 O7 P c1c2c(cc3c....
48 5ZGP - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
49 5ZGI - SIN C4 H6 O4 C(CC(=O)O)....
50 6D1G Ki = 34.2 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
51 5N4T ic50 = 1.06 uM R59 C15 H18 N2 O3 S C[C@H](CS)....
52 6DD0 Ki = 3.3 uM P9T C10 H7 F2 O5 P c1c(cc(c2c....
53 5Y6D ic50 = 54.8 nM 8PL C12 H14 F N O3 S C[C@H](CS)....
54 6RPN ic50 = 0.2 uM KDZ C16 H16 B O5 S [B-]1([C@H....
55 5FQC ic50 = 0.003 uM OK3 C17 H18 B N2 O6 [B-]1([C@H....
56 6TM9 ic50 = 0.23 uM 9NW C16 H21 Cl2 N5 O2 S c1cc(c(cc1....
57 5NI0 ic50 = 1.8 uM 8XW C14 H21 O4 P S CC(=O)SC[C....
58 5NHZ ic50 = 4.7 uM 8XZ C13 H19 O4 P S CC(=O)SC[C....
59 6JN6 Ki = 0.07 uM BY0 C14 H18 B N O4 S B([C@@H](C....
60 2WHG - FLC C6 H5 O7 C(C(=O)[O-....
61 5LCA ic50 = 32.8 uM B06 C16 H10 F3 N O3 c1cc(cc(c1....
62 6EW3 ic50 = 0.04 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
63 6O5T Ki = 0.316 uM L8J C10 H8 Br2 N O4 P c1c(cc(c2c....
64 5LSC ic50 = 20 uM 752 C18 H13 N5 O3 S2 c1ccc(c(c1....
65 6HF5 ic50 = 6.7 uM G1N C9 H7 N3 O4 S2 c1cc(cnc1)....
66 5ACW Kd = 145 uM RHU C4 H4 F3 N3 S Cn1c(nnc1S....
67 5LM6 ic50 = 7.7 uM H32 C15 H10 F N O4 c1cc2c(c(c....
68 6TGI Ki = 41 uM N8Z C9 H12 Cl N5 S CCn1c(nnc1....
69 5Y6E ic50 = 13.7 nM 8PO C12 H15 N O4 S C[C@H](CS)....
70 5MXR ic50 = 6.2 uM JTY C10 H8 N2 O4 S2 c1ccc(cc1)....
71 6SP7 ic50 = 0.026 uM K9B C19 H29 B N3 O6 [B-]1([C@H....
72 5LCH ic50 = 20.3 uM 6TU C19 H17 N O4 COc1cccc(c....
73 5MXQ ic50 = 1.9 uM U8K C12 H10 N2 O4 S c1ccc(cc1)....
74 6J8R Ki = 0.76 uM BHU C5 H12 B N O3 S B(CNC(=O)[....
75 2YZ3 Ki = 220 nM M5P C12 H16 O2 S c1ccc(cc1)....
76 5MM9 ic50 = 0.38 uM 8SH C15 H25 O3 P S CCOP(=O)([....
77 6YRP Kd = 389 nM PJB C17 H16 N4 O4 S COc1ccc(c(....
78 6DD1 Ki = 22.3 uM M3Q C10 H10 N O3 P c1cc2cccnc....
79 6ZGM - QKK C12 H11 F2 N7 O5 S2 [H]/N=C(N)....
80 5ACX Kd = 9 uM WL3 C14 H9 F O3 c1ccc(c(c1....
81 5LCF ic50 = 17.8 uM 6TJ C15 H11 N O3 c1ccc(cc1)....
82 5N4S ic50 = 0.055 uM R38 C15 H18 N2 O3 S C[C@H](CS)....
83 6V1P - QNA C10 H9 B F O5 [B-]1([C@@....
84 6EUM ic50 = 0.3 uM BY5 C9 H5 F3 O2 S c1cc(c(c(c....
85 6EWE ic50 = 3.1 uM C0W C11 H8 O2 S2 c1ccc2c(c1....
86 6F2N ic50 = 0.2 uM CF8 C20 H16 O2 S c1ccc2cc(c....
87 1MQO - CIT C6 H8 O7 C(C(=O)O)C....
88 5FQB ic50 = 0.3 uM OK3 C17 H18 B N2 O6 [B-]1([C@H....
89 4TYT ic50 = 0.02 uM S3C C9 H5 Cl3 O2 S c1cc(c(c(c....
90 5N55 Kd = 1.03 uM 8NN C21 H16 Cl N3 O4 c1ccc2c(c1....
91 5N58 Kd = 0.8 uM 93W C21 H16 Cl N3 O4 c1ccc2c(c1....
92 5LE1 ic50 = 10.6 uM 6UW C16 H11 Cl F N O3 c1cc2c(c(c....
93 6TMC ic50 = 0.53 uM NL5 C14 H19 N3 O3 S CC(C)OCc1c....
94 6R73 - LMP C17 H27 N3 O6 S C[C@H]1[C@....
95 6RZR - 8YF C12 H19 N3 O5 S [H]/N=C/NC....
96 6RZS - LHT C22 H27 N3 O8 S C[C@@H]1[C....
97 5NDB - 8TW C7 H8 Cl2 O4 S C1=S[C@H]2....
98 1JJT ic50 = 0.009 uM BDS C20 H18 O8 c1cc2c(cc1....
99 5EV8 - 3R9 C7 H11 N O2 S3 C1[C@@H](N....
100 3WXC - C93 C13 H15 N O5 c1cc(c(c(c....
101 2DOO Kd = 67 nM C4H C19 H27 N3 O3 S2 CN(C)c1ccc....
102 4F6Z - FLC C6 H5 O7 C(C(=O)[O-....
103 1DD6 - MCI C19 H19 N5 O3 S2 c1ccc(cc1)....
104 5EWA Ki = 15 uM 9BZ C9 H15 N O2 S3 CC1([C@H](....
105 1JJE ic50 = 0.0037 uM BYS C19 H18 O6 c1ccc(cc1)....
106 4UAM - FLC C6 H5 O7 C(C(=O)[O-....
107 4EXS Ki = 39 uM X8Z C9 H15 N O3 S C[C@H](CS)....
108 1M2X Ki ~ 85 uM MCO C9 H15 N O3 S C[C@H](CS)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: M5P; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 M5P 1 1
2 5PV 0.468085 0.625
3 DDW 0.446809 0.6
Similar Ligands (3D)
Ligand no: 1; Ligand: M5P; Similar ligands found: 68
No: Ligand Similarity coefficient
1 PHQ ALA 0.9225
2 1PS 0.9211
3 KPV 0.9193
4 XRS 0.9061
5 S0B 0.9033
6 HAR 0.9022
7 D4G 0.9003
8 JF5 0.8986
9 OJD 0.8938
10 AX4 0.8923
11 8CV 0.8914
12 11X 0.8909
13 CIR 0.8908
14 SB7 0.8889
15 37E 0.8887
16 ALY 0.8883
17 ZMG 0.8876
18 3KJ 0.8874
19 3CX 0.8873
20 S7V 0.8866
21 HHV 0.8858
22 NMM 0.8853
23 1KJ 0.8850
24 D53 0.8839
25 WT2 0.8837
26 0OP 0.8834
27 J9Y 0.8805
28 RE4 0.8802
29 6C4 0.8794
30 0OM 0.8792
31 2NP 0.8792
32 AOY 0.8786
33 2MR 0.8782
34 DA2 0.8776
35 IJ6 0.8771
36 26P 0.8767
37 AMJ 0.8755
38 PHQ DTH 0.8747
39 4JK 0.8735
40 3GC 0.8735
41 JFM 0.8728
42 C1E 0.8703
43 GHQ 0.8702
44 IEE 0.8700
45 EXY 0.8699
46 FZ3 0.8694
47 848 0.8688
48 3S9 0.8687
49 TPM 0.8669
50 6HN 0.8669
51 M3L 0.8667
52 RDY 0.8667
53 RDV 0.8662
54 ILO 0.8651
55 BSU 0.8650
56 PHQ DAL 0.8636
57 JOT 0.8627
58 0OO 0.8617
59 0V7 0.8615
60 BZM 0.8613
61 OGY 0.8613
62 RK4 0.8594
63 IJ1 0.8583
64 HPZ 0.8572
65 VIO 0.8548
66 L06 0.8546
67 0V8 0.8544
68 HJ1 0.8538
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FQC; Ligand: OK3; 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: 5fqc.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5FQC; Ligand: OK3; 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: 5fqc.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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