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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 NONCLASSICAL BETA-LACTAMASE INHIBITORS AGAINST EXTE DRUG RESISTANT STENOTROPHOMONAS MALTOPHILIA CLINICA ISOLATES. MOL. MICROBIOL. V. 106 492 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 NONCLASSICAL BETA-LACTAMASE INHIBITORS AGAINST EXTE DRUG RESISTANT STENOTROPHOMONAS MALTOPHILIA CLINICA ISOLATES. MOL. MICROBIOL. V. 106 492 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 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 32 families.
1 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
9 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
10 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
11 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
12 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
13 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
14 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
15 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
16 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
17 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
18 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
19 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
20 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
21 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
22 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
23 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
24 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
25 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
26 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
27 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
28 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
29 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
30 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
31 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
32 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
33 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
34 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
35 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
36 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
37 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
38 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
39 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
40 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
41 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
42 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 GGL 1 1
2 GLU 1 1
3 DGL 1 1
4 DGN 0.62963 0.821429
5 GLN 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 NPI 0.53125 0.923077
11 HGA 0.53125 0.666667
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 NVA 0.5 0.740741
17 API 0.5 0.884615
18 DAS 0.481481 0.846154
19 ASP 0.481481 0.846154
20 TNA 0.463415 0.685714
21 DBB 0.461538 0.692308
22 ABA 0.461538 0.692308
23 DSN 0.461538 0.655172
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 C2N 0.444444 0.666667
31 CYS 0.444444 0.642857
32 NLE 0.4375 0.689655
33 2HG 0.433333 0.653846
34 S2G 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 DLY 0.424242 0.666667
39 MED 0.424242 0.625
40 MET 0.424242 0.625
41 MSE 0.424242 0.606061
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 DHH 0.411765 0.851852
46 LYS 0.411765 0.645161
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 AS2 0.4 0.84
50 5OY 0.4 0.648649
51 ONH 0.4 0.611111
52 2JJ 0.4 0.648649
53 LEU 0.4 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NE2; Ligand: DGL; Similar sites found with APoc: 100
This union binding pocket(no: 1) in the query (biounit: 5ne2.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 1TID ATP None
2 4H8N NDP 1.43885
3 4GYS MLI 1.43885
4 3G5S FAD 1.79856
5 4AR8 IP8 GLY PRO ALA 1.79856
6 3H78 BE2 1.79856
7 2RCA GLY 2.15827
8 4OHU 2TK 2.15827
9 4OHU NAD 2.15827
10 1T7Q COA 2.15827
11 1T7Q 152 2.15827
12 3OEN GLU 2.15827
13 5BVE 4VG 2.15827
14 5CGE 51F 2.16606
15 2IHK CSF 2.51799
16 4B7X NAP 2.51799
17 2AQX ATP 2.51799
18 5T79 NDP 2.51799
19 1NAA 6FA 2.51799
20 1QX4 FAD 2.55474
21 4ZFL 4NK 2.5641
22 1C96 FLC 2.8777
23 3PPM JG1 2.8777
24 2RCU BUJ 2.8777
25 2YJP CYS 2.8777
26 4CP8 MLI 2.8777
27 5KF9 ACO 2.8777
28 2RC8 DSN 2.8777
29 3PC3 P1T 2.8777
30 4I4Z 2NE 2.8777
31 5O0B 9FE 3.08642
32 1JOC ITP 3.2
33 1YQS BSA 3.23741
34 2PI8 NAG NAG NAG NAG NAG NAG 3.23741
35 5GM9 CBK 3.28639
36 5GM9 CBI 3.28639
37 1NNU TCT 3.33333
38 1V0C ACO 3.46535
39 3C56 PH4 3.58306
40 2WYA HMG 3.59712
41 1XPK HMG 3.59712
42 3Q9T FAY 3.59712
43 3VC3 C6P 3.59712
44 5M1T C2E 3.59712
45 3GBR PRP 3.59712
46 2DM6 IMN 3.95683
47 2DM6 NAP 3.95683
48 3KJD 78P 3.95683
49 3OTH TYD 3.95683
50 4KQR VPP 3.95683
51 1E3I CXF 3.95683
52 2EFX NFA 3.95683
53 4B2G V1N 3.95683
54 3OZ2 FAD 4.03023
55 2FLI DX5 4.09091
56 3IHB GLU 4.31655
57 3NYQ AMP 4.31655
58 3NYQ MCA 4.31655
59 1Q19 APC 4.31655
60 5BRT FAD 4.31655
61 3HLF SIM 4.31655
62 3P3G UKW 4.31655
63 3P3G 3P3 4.31655
64 4LS7 1X9 4.31655
65 4D42 NAP 4.67626
66 4D42 W0I 4.67626
67 5F2T PLM 5.03597
68 5J47 6JJ 5.03597
69 4OKE AMP 5.35714
70 5F2K OCA 5.39568
71 5F2K SAH 5.39568
72 5K8B PDG 5.39568
73 4IWN GEK 5.7554
74 1L5J TRA 6.11511
75 1QF5 GDP 6.11511
76 1QF5 RPL 6.11511
77 1Q1Y BB2 6.28272
78 5HWO HMG 6.47482
79 3EAU NDP 6.47482
80 3EAU PDN 6.47482
81 4JTA NAP 6.47482
82 3HUN ZZ7 6.83453
83 4HSE ADP 6.83453
84 3VEH 0GA 6.83453
85 4I42 1HA 7.01754
86 4JWX 1N4 7.19424
87 4I06 X8A 8.16993
88 1GZF ADP 8.53081
89 1GZF NAD 8.53081
90 3WG6 NDP 8.99281
91 3PNL ADP 9.00474
92 4LRZ ADP 9.00474
93 3I7V B4P 9.70149
94 3GDN FAD 11.1511
95 3GDN HBX 11.1511
96 1XVB 3BR 12.5899
97 4K91 SIN 15.1079
98 3QLM PLM 15.3226
99 3ZLR X0B 18.3544
100 4WB7 ATP 30
Pocket No.: 2; Query (leader) PDB : 5NE2; Ligand: DGL; Similar sites found with APoc: 40
This union binding pocket(no: 2) in the query (biounit: 5ne2.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4EKQ NPO None
2 3OJF IMJ 1.16732
3 3OJF NDP 1.16732
4 4JB1 NAP 1.79856
5 4DQL FAD 2.15827
6 3OZV FAD 2.51799
7 4M52 FAD 2.51799
8 4M52 M52 2.51799
9 5W19 9TD 2.51799
10 2A8X FAD 2.51799
11 6CEP OXM 2.8777
12 6CEP NAD 2.8777
13 5LU5 M7P 3.04569
14 1QG6 NAD 3.06513
15 5GZ6 NDP 3.23741
16 5GZ6 7C3 3.23741
17 5JY4 ISC 3.59712
18 2ZB3 NDP 3.59712
19 5JXZ ISJ 3.59712
20 5JXZ ISC 3.59712
21 6EXF LYS 3.95683
22 2FN1 SAL 4.31655
23 2B99 RDL 4.48718
24 3LSJ COA PLM 4.54545
25 3LSJ PLM COA 4.54545
26 1I2L DCS 4.67626
27 5LD8 6U5 5.03597
28 6IS0 SAH 5.03597
29 3V91 UPG 5.03597
30 4A0S NAP 6.47482
31 2PHN GDP 7.48031
32 5Z99 SLB 7.62887
33 6FHO FAD 7.76942
34 2VBA P4T 8.99281
35 1BZL GCG 8.99281
36 2H92 C5P 10.0457
37 3JYN NDP 10.4317
38 5W1E PHB 11.5108
39 3R75 BEZ 11.5108
40 5BUK FAD 11.8705
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