Receptor
PDB id Resolution Class Description Source Keywords
6NJ0 1.83 Å EC: 6.2.1.26 WILD-TYPE E. COLI MENE WITH BOUND M PHENYLETHER-LINKED ANALO OSB-AMS ESCHERICHIA COLI (STRAIN K12) MENE E. COLI MENAQUINONE LIGASE
Ref.: STRUCTURE-BASED DESIGN, SYNTHESIS, AND BIOLOGICAL E OF NON-ACYL SULFAMATE INHIBITORS OF THE ADENYLATE-F ENZYME MENE. BIOCHEMISTRY V. 58 1918 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KOY A:501;
 Valid;
 none;
 ic50 = 8.1 uM
519.506 C26 H25 N5 O7 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5C5H 2.4 Å EC: 6.2.1.26 R195K E. COLI MENE WITH BOUND OSB-AMS ESCHERICHIA COLI (STRAIN K12) LIGASE
Ref.: MECHANISM OF MENE INHIBITION BY ACYL-ADENYLATE ANAL DISCOVERY OF NOVEL ANTIBACTERIAL AGENTS. BIOCHEMISTRY V. 54 6514 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
2 6NJ0 ic50 = 8.1 uM KOY C26 H25 N5 O7 c1ccc(c(c1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
2 6NJ0 ic50 = 8.1 uM KOY C26 H25 N5 O7 c1ccc(c(c1....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
2 6NJ0 ic50 = 8.1 uM KOY C26 H25 N5 O7 c1ccc(c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KOY; Similar ligands found: 178
No: Ligand ECFP6 Tc MDL keys Tc
1 KOY 1 1
2 4YB 0.628319 0.767442
3 SON 0.528846 0.818182
4 3UK 0.513043 0.878378
5 B5V 0.495726 0.891892
6 KG4 0.490741 0.828947
7 AMP 0.490196 0.8
8 A 0.490196 0.8
9 5AL 0.482143 0.84
10 CA0 0.481481 0.828947
11 AOC 0.480769 0.857143
12 DLL 0.478632 0.864865
13 45A 0.47619 0.779221
14 A2D 0.47619 0.826667
15 ABM 0.47619 0.779221
16 LMS 0.475728 0.72619
17 B1U 0.47541 0.703297
18 OOB 0.474138 0.864865
19 SRA 0.471154 0.759494
20 8LE 0.469027 0.807692
21 649 0.46875 0.730337
22 ADX 0.46789 0.72619
23 M33 0.46789 0.792208
24 BA3 0.46729 0.826667
25 AP2 0.46729 0.772152
26 A12 0.46729 0.772152
27 FYA 0.466667 0.792208
28 8LQ 0.465517 0.818182
29 OZP 0.464567 0.851351
30 G5A 0.464286 0.704545
31 50T 0.463636 0.769231
32 B4P 0.462963 0.826667
33 AP5 0.462963 0.826667
34 ADP 0.462963 0.802632
35 GAP 0.460177 0.828947
36 PRX 0.459459 0.782051
37 APC 0.459459 0.772152
38 9SN 0.459016 0.833333
39 AN2 0.458716 0.792208
40 AT4 0.458716 0.772152
41 WAQ 0.458333 0.820513
42 GSU 0.458333 0.744186
43 DSZ 0.457627 0.724138
44 VMS 0.456897 0.712644
45 54H 0.456897 0.712644
46 FA5 0.455285 0.842105
47 B5M 0.455285 0.88
48 AU1 0.454545 0.782051
49 F0P 0.453846 0.851351
50 A5A 0.452174 0.729412
51 H1Q 0.45045 0.789474
52 ATP 0.45045 0.802632
53 HEJ 0.45045 0.802632
54 ACP 0.45045 0.782051
55 5AS 0.449541 0.685393
56 SSA 0.448276 0.704545
57 SRP 0.448276 0.818182
58 8LH 0.448276 0.818182
59 ACQ 0.447368 0.782051
60 AQP 0.446429 0.802632
61 AR6 0.446429 0.826667
62 5FA 0.446429 0.802632
63 APR 0.446429 0.826667
64 PR8 0.446281 0.790123
65 ADP MG 0.445455 0.824324
66 PAJ 0.445378 0.777778
67 AMO 0.445378 0.818182
68 52H 0.444444 0.704545
69 5CD 0.444444 0.84058
70 B5Y 0.443548 0.88
71 8PZ 0.443548 0.724138
72 YAP 0.443548 0.855263
73 XYA 0.443299 0.855072
74 RAB 0.443299 0.855072
75 ADN 0.443299 0.855072
76 1ZZ 0.442623 0.780488
77 9K8 0.442623 0.738636
78 AGS 0.442478 0.7625
79 ADV 0.442478 0.794872
80 AD9 0.442478 0.782051
81 ADP PO3 0.442478 0.824324
82 ATP MG 0.442478 0.824324
83 A5D 0.442478 0.819444
84 SAP 0.442478 0.7625
85 RBY 0.442478 0.794872
86 NVA LMS 0.441667 0.7
87 00A 0.441667 0.820513
88 S0N 0.440789 0.75
89 TSB 0.440678 0.72093
90 8X1 0.440678 0.7
91 5CA 0.440678 0.704545
92 53H 0.440678 0.704545
93 YSA 0.44 0.744186
94 LEU LMS 0.438017 0.681319
95 DQV 0.4375 0.84
96 9ZD 0.436975 0.797468
97 9ZA 0.436975 0.797468
98 8QN 0.436975 0.84
99 TYR AMP 0.436508 0.855263
100 TAT 0.434783 0.772152
101 ANP 0.434783 0.782051
102 T99 0.434783 0.772152
103 LAD 0.434426 0.8
104 KAA 0.434426 0.7
105 5N5 0.434343 0.828571
106 4AD 0.433333 0.807692
107 LSS 0.433333 0.688889
108 NSS 0.433333 0.704545
109 HQG 0.432203 0.815789
110 TXA 0.430894 0.818182
111 ME8 0.430894 0.780488
112 3OD 0.430894 0.828947
113 A4D 0.43 0.828571
114 APC MG 0.429825 0.802632
115 AHX 0.429752 0.765432
116 7MD 0.429688 0.780488
117 DAL AMP 0.428571 0.84
118 NXX 0.427481 0.842105
119 DND 0.427481 0.842105
120 ATF 0.42735 0.772152
121 ADP ALF 0.42735 0.7625
122 ALF ADP 0.42735 0.7625
123 DTA 0.427184 0.819444
124 A6D 0.42623 0.728395
125 OAD 0.42623 0.828947
126 AMP DBH 0.425197 0.853333
127 5SV 0.425 0.743902
128 5X8 0.424779 0.84507
129 TYM 0.424242 0.842105
130 WSA 0.424242 0.732558
131 6YZ 0.423729 0.782051
132 SMM 0.423729 0.775
133 MTA 0.423077 0.805556
134 P5A 0.422764 0.692308
135 ADQ 0.421488 0.828947
136 A3R 0.421488 0.753086
137 8Q2 0.421053 0.719101
138 DZD 0.42029 0.777778
139 NB8 0.419355 0.7875
140 PTJ 0.419355 0.7875
141 EP4 0.417476 0.783784
142 MAP 0.416667 0.7625
143 NAX 0.416667 0.790123
144 A22 0.416667 0.815789
145 KB1 0.416 0.815789
146 MYR AMP 0.416 0.780488
147 TAD 0.415385 0.756098
148 3DH 0.415094 0.805556
149 9X8 0.414634 0.78481
150 A3P 0.414414 0.8
151 4UV 0.414062 0.831169
152 SAI 0.413793 0.835616
153 M2T 0.413462 0.763158
154 25A 0.413223 0.826667
155 OZV 0.413223 0.802632
156 SFG 0.412281 0.857143
157 LAQ 0.412214 0.780488
158 ADP VO4 0.411765 0.792208
159 VO4 ADP 0.411765 0.792208
160 A A 0.41129 0.802632
161 7C5 0.410853 0.902778
162 7MC 0.410448 0.761905
163 A1R 0.409836 0.753086
164 ATP A 0.409449 0.837838
165 ATP A A A 0.409449 0.837838
166 48N 0.409091 0.7875
167 M24 0.408451 0.8125
168 4UU 0.407692 0.831169
169 XAH 0.40625 0.759036
170 NAI 0.406015 0.797468
171 6V0 0.406015 0.7875
172 SA8 0.405172 0.802632
173 SLU 0.404255 0.735632
174 6RE 0.40367 0.766234
175 MAO 0.401786 0.743902
176 SAH 0.401709 0.847222
177 AHZ 0.401515 0.802469
178 YLB 0.4 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5C5H; Ligand: 4YB; 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: 5c5h.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5C5H; Ligand: 4YB; 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: 5c5h.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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