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Receptor
PDB id Resolution Class Description Source Keywords
4DE2 1.4 Å EC: 3.5.2.6 CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 12 ESCHERICHIA COLI CTX-M MOLECULAR DOCKING FRAGMENT HYDROLASE-HYDROLASE INHICOMPLEX
Ref.: STRUCTURE-BASED DESIGN OF POTENT AND LIGAND-EFFICIE INHIBITORS OF CTX-M CLASS A BETA-LACTAMASE J.MED.CHEM. V. 55 2163 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS B:303;
B:304;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
DN3 A:301;
A:302;
B:301;
B:302;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 76 uM
322.364 C17 H18 N6 O CN(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DE2 1.4 Å EC: 3.5.2.6 CTX-M-9 CLASS A BETA-LACTAMASE COMPLEXED WITH COMPOUND 12 ESCHERICHIA COLI CTX-M MOLECULAR DOCKING FRAGMENT HYDROLASE-HYDROLASE INHICOMPLEX
Ref.: STRUCTURE-BASED DESIGN OF POTENT AND LIGAND-EFFICIE INHIBITORS OF CTX-M CLASS A BETA-LACTAMASE J.MED.CHEM. V. 55 2163 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 4DE2 Ki = 76 uM DN3 C17 H18 N6 O CN(C)Cc1cc....
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 4DE2 Ki = 76 uM DN3 C17 H18 N6 O CN(C)Cc1cc....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4DE2 Ki = 76 uM DN3 C17 H18 N6 O CN(C)Cc1cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DN3; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 DN3 1 1
2 F13 0.642857 0.696429
3 DN8 0.642857 0.696429
4 DN6 0.616438 0.684211
5 0J7 0.576923 0.735849
6 0J6 0.518072 0.735849
7 0JB 0.47619 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DE2; Ligand: DN3; Similar sites found with APoc: 159
This union binding pocket(no: 1) in the query (biounit: 4de2.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4OAS 2SW None
2 5Y24 GLY MET PRO ARG GLY ALA None
3 3WR7 COA None
4 4MGB XDH None
5 4MG7 27H None
6 5DX3 EST None
7 3UUA 0CZ None
8 1YYE 196 1.14068
9 1U3R 338 1.24481
10 2YJD YJD 1.25
11 4U9W COA 1.44928
12 3WCA FPS 1.52091
13 4OKZ 3E9 1.52091
14 5K13 6Q7 1.62602
15 5F2T PLM 1.90114
16 4HY1 19X 1.90114
17 1SOW NAD 1.90114
18 1QXO FMN 1.90114
19 5G57 6M5 1.90114
20 5N2I NAP 2.15517
21 3SQP FAD 2.28137
22 2PX6 DH9 2.28137
23 5BVE 4VG 2.28137
24 3P5P A3C 2.28137
25 3ABI NAD 2.28137
26 1EE4 PRO ALA ALA LYS ARG VAL LYS LEU ASP 2.28137
27 2VL8 CTS 2.28137
28 2CB3 MLD 2.28571
29 1DB1 VDX 2.3166
30 1ATL 0QI 2.47525
31 4AIG FLX 2.48756
32 2CNT COA 2.5
33 1XNG DND 2.61194
34 4M52 M52 2.6616
35 5LGA 6VH 2.6616
36 5TUX ECH 2.6616
37 2JFN UMA 2.6616
38 4Q0A 4OA 2.6616
39 4KBS PX2 2.7907
40 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 2.89256
41 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 3
42 3AAQ ARU 3.04183
43 3OV6 MK0 3.04183
44 5DEY 59T 3.04183
45 1UXG FUM 3.04183
46 1UXG NAD 3.04183
47 1WPQ NAD 3.04183
48 1N1G BCP 3.04183
49 5GUE GGS 3.32326
50 4R57 ACO 3.40909
51 1J78 VDY 3.42205
52 2JJK R15 3.42205
53 1N20 3AG 3.42205
54 3H78 BE2 3.42205
55 3E9I XAH 3.42205
56 3EFV NAD 3.4632
57 5XJ8 NKO 3.48259
58 5MFI LYS ARG LYS ARG LYS ARG LYS ARG 3.7037
59 5D9O BGC BGC BGC BGC 3.80228
60 4PLG NAI 3.80228
61 4PLG OXM 3.80228
62 5B0W 22B 3.80228
63 2HJR APR 3.80228
64 6BMS POV 3.80228
65 1PZG A3D 3.80228
66 1GHE ACO 3.9548
67 4DV8 0LX 4.18251
68 4PLT NAI 4.18251
69 4PLT OXM 4.18251
70 1U1I NAD 4.18251
71 2VBQ BSJ 4.24242
72 6FTB M0E 4.28571
73 1H0A I3P 4.43038
74 5CXI 5TW 4.4335
75 3L9R L9Q 4.56274
76 2ZPA ACO 4.56274
77 3L9R L9R 4.56274
78 3GFB NAD 4.56274
79 6ARJ SAH 4.56274
80 1W5T ANP 4.56274
81 4ETZ C2E 4.56274
82 4RHP PEF 4.68085
83 6F70 GSH 4.7619
84 4QVX 3CQ 4.79042
85 5X3R 7Y3 4.87805
86 3HR1 PF9 4.94297
87 3AYI HCI 4.94297
88 3AYI FAD 4.94297
89 2VZZ SCA 5.04587
90 4H07 IPH 5.19481
91 4WQ2 3SU 5.20231
92 4XU6 TDA 5.2381
93 5G5G MCN 5.24017
94 1O6Z NAD 5.28053
95 5MW4 5JU 5.32319
96 6C1R EFD 5.32319
97 3L0E G58 5.5336
98 3KFC 61X 5.5336
99 2BTO GTP 5.55556
100 3D04 SAK 5.66038
101 3ZLR X0B 5.6962
102 5BQS 4VN 5.70342
103 2Q8M AMP 5.70342
104 3ET1 ET1 5.70342
105 3MBG FAD 5.7554
106 2Z77 HE7 5.7554
107 1QK3 5GP 6.00858
108 5N69 2OW 6.03015
109 5BNS 4VM 6.08365
110 3VRV YSD 6.08365
111 1QX4 FAD 6.08365
112 1EBL COA 6.08365
113 5VZ0 2BA 6.08365
114 3FAL LO2 6.19835
115 2HJ3 FAD 6.4
116 1N62 MCN 6.46388
117 4I4B NAD 6.46388
118 1UUO BRF 6.46388
119 4I4B 1CV 6.46388
120 3EWC MCF 6.46388
121 2FAH GDP 6.46388
122 5HMY LNY 6.46388
123 4CRZ ACO 6.56934
124 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 6.62983
125 2YPO PHE 6.84411
126 5OLK DTP 6.84411
127 3DZT EAH 7.60456
128 4WN5 MVC 7.82609
129 3G08 FEE 7.98479
130 4A0S CO8 7.98479
131 3PF7 MLA 7.98479
132 5HZ9 5M8 8.14815
133 2WPX ACO 8.25959
134 5OSW DIU 8.36502
135 1GUZ NAD 8.74525
136 1BZL GCG 9.12547
137 3D78 NBB 9.2437
138 1KZN CBN 9.26829
139 5CSD ACD 9.43396
140 2PSM BAM 10.7438
141 5C9J STE 11.0266
142 2WPW ACO 11.2094
143 1T27 PCW 11.4068
144 3ZJ0 ACO 12.1359
145 5ODQ FAD 13.587
146 6GL8 F3Q 13.9535
147 1EU1 MGD 14.0684
148 2A9G ARG 14.4487
149 5XDT GDP 14.4487
150 5XDT MB3 14.4487
151 4DOO DAO 14.6341
152 5ZCO TGL 15.2941
153 5W97 CHD 15.2941
154 5Z84 TGL 15.2941
155 2DYR TGL 15.2941
156 5LS7 ACO 17.0732
157 4ZSY RW2 19.3916
158 5M45 AMP 20.1521
159 2Y69 CHD 23.7113
Pocket No.: 2; Query (leader) PDB : 4DE2; Ligand: DN3; Similar sites found with APoc: 40
This union binding pocket(no: 2) in the query (biounit: 4de2.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4USI ATP None
2 1NU4 MLA None
3 1V35 NAI 1.82371
4 3HUN ZZ7 1.90114
5 2IMP NAI 1.90114
6 4WGF HX2 1.95122
7 4ZFL 4NK 2.5641
8 5M3E APR 3.0303
9 3ORK AGS 3.04183
10 6CGD GNP 3.04183
11 6CGD AKN 3.04183
12 4Y30 SAH 3.04183
13 4Y30 49L 3.04183
14 3IES M24 3.04183
15 4CS4 ANP 3.42205
16 3UEC ALA ARG TPO LYS 3.42466
17 4CNK FAD 3.80228
18 1YQS BSA 4.18251
19 4KQR VPP 4.18251
20 1RHC F42 ACN 4.56274
21 3W8X FTK 4.56274
22 3W8X FAD 4.56274
23 2EFX NFA 4.56274
24 1C3X 8IG 4.94297
25 3TCT 3MI 5.51181
26 4CBU ATP 5.70342
27 3I7V B4P 5.97015
28 3SM2 478 6.81818
29 3IHB GLU 7.22433
30 5EXE 5SR 7.22433
31 2YAK OSV 7.98479
32 1JOC ITP 8
33 4K91 SIN 8.36502
34 1QM5 GLC GLC GLC PO4 SGC GLC 9.12547
35 2VGK REZ 10.2662
36 3NOJ PYR 13.0252
37 6C8X BVR 14.1414
38 5TVF PUT 21.1765
39 5TVM PUT 21.1765
40 4OKE AMP 23.2143
Pocket No.: 3; Query (leader) PDB : 4DE2; Ligand: DN3; Similar sites found with APoc: 59
This union binding pocket(no: 3) in the query (biounit: 4de2.bio2) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZZ6 NAD None
2 2HF9 GSP 1.32743
3 4PVR ASP 1.90114
4 5KKA 6V0 1.90114
5 2X1L ADN 1.90114
6 2DM6 IMN 1.90114
7 2DM6 NAP 1.90114
8 5K9B FMN 2.22222
9 3CAQ NDP 2.28137
10 2YK7 CSF 2.28137
11 3KRB NAP 2.6616
12 1VBJ NAP 2.6616
13 4YRY FAD 2.6616
14 4YRY NAD 2.6616
15 3FJO FMN 2.6616
16 4BLW AMP 2.6616
17 4BLW SAH 2.6616
18 4Y4V DAL 2.6616
19 1F8G NAD 2.6616
20 2OM2 GDP 2.6616
21 2QIA U20 2.67176
22 2C29 NAP 3.04183
23 4OXX FMN 3.08642
24 1D1Q 4NP 3.10559
25 4DHY S41 3.41151
26 2QRK AMP 3.42205
27 1LVW TYD 3.42205
28 3NTY NAP 3.80228
29 3NTY 5P3 3.80228
30 1Q3Q ANP 3.83212
31 3OJF NDP 3.89105
32 3EYA FAD 4.18251
33 1RRM APR 4.18251
34 3AB4 THR 4.49438
35 3IB8 AMP 4.56274
36 5JCA NDP 4.56274
37 1QHG ATP 4.56274
38 4ZH7 FUC GAL NAG GAL FUC 4.94297
39 1G0N NDP 5.32319
40 1C1X NAD 5.70342
41 1CDO NAD 5.70342
42 1BXG NAD 5.70342
43 4BMO FMN 5.88235
44 5F7N NAG GAL FUC FUC A2G 6.08365
45 5F7Y GLC GAL NAG GAL FUC A2G 6.08365
46 1TLL FMN 6.46388
47 1MFD GLA MMA ABE 7.30594
48 5AHS COA 7.98479
49 1OIX GDP 9.42408
50 4FZV SAM 9.88593
51 4C5N ACP 9.88593
52 3H7U NAP 10.2662
53 4H2D FMN 10.303
54 5CB3 APR 10.3825
55 5UXF 2BA 10.6464
56 3FQ8 PMP 11.0266
57 1CLU DBG 11.4458
58 3U7S 017 13.1313
59 2FCR FMN 13.8728
Pocket No.: 4; Query (leader) PDB : 4DE2; Ligand: DN3; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 4de2.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3AI3 SOE 4.56274
2 2A42 ATP 6.15385
3 1XHC FAD 10.2662
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