Receptor
PDB id Resolution Class Description Source Keywords
5NE2 1.19 Å EC: 3.5.2.6 L2 CLASS A SERINE-BETA-LACTAMASE STENOTROPHOMONAS MALTOPHILIA BETA-LACTAMASE CARBAPENEMASE HYDROLASE
Ref.: STRUCTURAL/MECHANISTIC INSIGHTS INTO THE EFFICACY O NON-CLASSICAL BETA-LACTAMASE INHIBITORS AGAINST EXT DRUG RESISTANT STENOTROPHOMONAS MALTOPHILIA CLINICA ISOLATES. MOL. MICROBIOL. 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DGL A:301;
B:301;
Valid;
Valid;
none;
none;
Ki = 84 pM
147.129 C5 H9 N O4 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NE2 1.19 Å EC: 3.5.2.6 L2 CLASS A SERINE-BETA-LACTAMASE STENOTROPHOMONAS MALTOPHILIA BETA-LACTAMASE CARBAPENEMASE HYDROLASE
Ref.: STRUCTURAL/MECHANISTIC INSIGHTS INTO THE EFFICACY O NON-CLASSICAL BETA-LACTAMASE INHIBITORS AGAINST EXT DRUG RESISTANT STENOTROPHOMONAS MALTOPHILIA CLINICA ISOLATES. MOL. MICROBIOL. 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
7 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
8 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
9 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
10 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
11 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
12 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
13 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
14 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
15 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
16 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
17 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
18 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
19 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
20 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
21 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
22 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
23 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
24 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
25 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
26 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
27 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
28 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
29 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
30 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
31 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
32 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DGL; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU 1 1
2 DGL 1 1
3 GGL 1 1
4 GLN 0.62963 0.821429
5 DGN 0.62963 0.821429
6 ONL 0.586207 0.821429
7 UN1 0.566667 0.96
8 11C 0.566667 0.96
9 HCS 0.555556 0.714286
10 HGA 0.53125 0.666667
11 NPI 0.53125 0.923077
12 HSE 0.518519 0.758621
13 DAB 0.518519 0.666667
14 MEQ 0.515152 0.71875
15 3O3 0.513514 0.727273
16 API 0.5 0.884615
17 NVA 0.5 0.740741
18 ASP 0.481481 0.846154
19 DAS 0.481481 0.846154
20 TNA 0.463415 0.685714
21 ABA 0.461538 0.692308
22 DSN 0.461538 0.655172
23 DBB 0.461538 0.692308
24 SER 0.461538 0.655172
25 RGP 0.459459 0.648649
26 ORN 0.451613 0.689655
27 HOZ 0.451613 0.666667
28 AE5 0.447368 0.727273
29 DCY 0.444444 0.642857
30 CYS 0.444444 0.642857
31 C2N 0.444444 0.666667
32 NLE 0.4375 0.689655
33 S2G 0.433333 0.653846
34 2HG 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 MET 0.424242 0.625
39 MSE 0.424242 0.606061
40 DLY 0.424242 0.666667
41 MED 0.424242 0.625
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 LYS 0.411765 0.645161
46 DHH 0.411765 0.851852
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 LEU 0.4 0.642857
50 5OY 0.4 0.648649
51 AS2 0.4 0.84
52 2JJ 0.4 0.648649
53 ONH 0.4 0.611111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NE2; Ligand: DGL; Similar sites found: 51
This union binding pocket(no: 1) in the query (biounit: 5ne2.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4H8N NDP 0.03943 0.41367 1.43885
2 1R6W 164 0.03359 0.41146 1.43885
3 4GYS MLI 0.006454 0.40367 1.43885
4 3G5S FAD 0.02866 0.41725 1.79856
5 3H78 BE2 0.03641 0.40814 1.79856
6 2RCA GLY 0.00396 0.41899 2.15827
7 3OEN GLU 0.008925 0.41155 2.15827
8 3A2Q ACA ACA 0.02804 0.42292 2.51799
9 4B7X NAP 0.02525 0.41731 2.51799
10 1C96 FLC 0.004026 0.43341 2.8777
11 2RC8 DSN 0.003165 0.41959 2.8777
12 4CP8 MLI 0.006722 0.41333 2.8777
13 1N4W FAD 0.02962 0.40847 2.8777
14 3FMI KAP 0.0118 0.42576 3.18725
15 1JOC ITP 0.004029 0.42508 3.2
16 1YQS BSA 0.0001567 0.54086 3.23741
17 2PI8 NAG NAG NAG NAG NAG NAG 0.04626 0.40287 3.23741
18 5GM9 CBI 0.006115 0.42046 3.28639
19 5GM9 CBK 0.01311 0.42046 3.28639
20 2DVZ GLU 0.009622 0.44644 3.50318
21 2WYA HMG 0.0157 0.42211 3.59712
22 1XPK HMG 0.02241 0.41827 3.59712
23 3VC3 C6P 0.02658 0.40106 3.59712
24 4KQR VPP 0.000009318 0.58385 3.95683
25 2EFX NFA 0.0001413 0.52519 3.95683
26 2DM6 IMN 0.0272 0.42275 3.95683
27 3KJD 78P 0.02602 0.41358 3.95683
28 3OTH TYD 0.0158 0.41065 3.95683
29 4B2G V1N 0.02836 0.40139 3.95683
30 3NYQ MCA 0.006342 0.44264 4.31655
31 3NYQ AMP 0.00664 0.44264 4.31655
32 1Q19 APC 0.02651 0.41205 4.31655
33 3P3G 3P3 0.03554 0.40418 4.31655
34 3P3G UKW 0.03554 0.40418 4.31655
35 4LS7 1X9 0.01451 0.40379 4.31655
36 4D42 W0I 0.01051 0.45543 4.67626
37 4D42 NAP 0.01051 0.45543 4.67626
38 5K8B PDG 0.01915 0.40362 5.39568
39 1L5J TRA 0.003332 0.42299 6.11511
40 3HUN ZZ7 0.0000005883 0.50721 6.83453
41 4HSE ADP 0.01435 0.40538 6.83453
42 3VEH 0GA 0.03673 0.40351 6.83453
43 3PNL ADP 0.02583 0.40417 9.00474
44 4LRZ ADP 0.02755 0.40166 9.00474
45 4LOK 1YD 0.02255 0.42417 10.6383
46 3GDN FAD 0.02851 0.40597 11.1511
47 3GDN HBX 0.03575 0.40597 11.1511
48 1XVB 3BR 0.01082 0.41353 12.5899
49 4K91 SIN 0.00002625 0.521 15.1079
50 3DCM SAM 0.03168 0.42494 15.625
51 3ZLR X0B 0.0414 0.40534 18.3544
Pocket No.: 2; Query (leader) PDB : 5NE2; Ligand: DGL; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 5ne2.bio2) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4EKQ NPO 0.0115 0.41692 None
2 3OZV FAD 0.04796 0.41477 2.51799
3 4M52 FAD 0.02913 0.41043 2.51799
4 3OVR 5SP 0.008198 0.41945 2.63158
5 5JY4 ISC 0.003695 0.42366 3.59712
6 5JXZ ISJ 0.008151 0.40135 3.59712
7 5JXZ ISC 0.008822 0.40135 3.59712
8 3LSJ COA PLM 0.02342 0.40879 4.54545
9 3LSJ PLM COA 0.03239 0.40198 4.54545
10 2PHN GDP 0.01704 0.41383 7.48031
11 2VBA P4T 0.001008 0.47671 8.99281
12 5BUK FAD 0.0432 0.40846 11.8705
13 1HN4 MJI 0.02496 0.4302 14.5038
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