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 Kd = 394 nM 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 Kd = 394 nM 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 Kd = 394 nM 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 (2D)
Ligand no: 1; Ligand: KOY; Similar ligands found: 189
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 V2G 0.495495 0.7875
7 KG4 0.490741 0.828947
8 A 0.490196 0.8
9 AMP 0.490196 0.8
10 AMP MG 0.485437 0.810811
11 5AL 0.482143 0.84
12 CA0 0.481481 0.828947
13 AOC 0.480769 0.857143
14 DLL 0.478632 0.864865
15 A2D 0.47619 0.826667
16 45A 0.47619 0.779221
17 ABM 0.47619 0.779221
18 LMS 0.475728 0.72619
19 B1U 0.47541 0.703297
20 OOB 0.474138 0.864865
21 V47 0.473684 0.925373
22 SRA 0.471154 0.759494
23 8LE 0.469027 0.807692
24 649 0.46875 0.730337
25 M33 0.46789 0.792208
26 ADX 0.46789 0.72619
27 AP2 0.46729 0.772152
28 BA3 0.46729 0.826667
29 A12 0.46729 0.772152
30 FYA 0.466667 0.792208
31 8LQ 0.465517 0.818182
32 OZP 0.464567 0.851351
33 G5A 0.464286 0.704545
34 50T 0.463636 0.769231
35 ADP 0.462963 0.802632
36 B4P 0.462963 0.826667
37 AP5 0.462963 0.826667
38 QXP 0.461538 0.729412
39 GAP 0.460177 0.828947
40 PRX 0.459459 0.782051
41 APC 0.459459 0.772152
42 9SN 0.459016 0.833333
43 AN2 0.458716 0.792208
44 AT4 0.458716 0.772152
45 GSU 0.458333 0.744186
46 WAQ 0.458333 0.820513
47 DSZ 0.457627 0.724138
48 VMS 0.456897 0.712644
49 54H 0.456897 0.712644
50 B5M 0.455285 0.88
51 FA5 0.455285 0.842105
52 AU1 0.454545 0.782051
53 F0P 0.453846 0.851351
54 A5A 0.452174 0.729412
55 HEJ 0.45045 0.802632
56 ACP 0.45045 0.782051
57 ATP 0.45045 0.802632
58 H1Q 0.45045 0.789474
59 5AS 0.449541 0.685393
60 SRP 0.448276 0.818182
61 8LH 0.448276 0.818182
62 SSA 0.448276 0.704545
63 ACQ 0.447368 0.782051
64 AQP 0.446429 0.802632
65 5FA 0.446429 0.802632
66 APR 0.446429 0.826667
67 AR6 0.446429 0.826667
68 PR8 0.446281 0.790123
69 ADP MG 0.445455 0.824324
70 ADP BEF 0.445455 0.824324
71 PAJ 0.445378 0.777778
72 AMO 0.445378 0.818182
73 5CD 0.444444 0.84058
74 52H 0.444444 0.704545
75 B5Y 0.443548 0.88
76 8PZ 0.443548 0.724138
77 XYA 0.443299 0.855072
78 ADN 0.443299 0.855072
79 RAB 0.443299 0.855072
80 9K8 0.442623 0.738636
81 1ZZ 0.442623 0.780488
82 A5D 0.442478 0.819444
83 ADV 0.442478 0.794872
84 AGS 0.442478 0.7625
85 ADP PO3 0.442478 0.824324
86 AD9 0.442478 0.782051
87 ATP MG 0.442478 0.824324
88 RBY 0.442478 0.794872
89 NVA LMS 0.441667 0.7
90 00A 0.441667 0.820513
91 S0N 0.440789 0.75
92 TSB 0.440678 0.72093
93 5CA 0.440678 0.704545
94 8X1 0.440678 0.7
95 QA7 0.440678 0.807692
96 53H 0.440678 0.704545
97 YSA 0.44 0.744186
98 VO4 ADP 0.439655 0.782051
99 QXG 0.438017 0.741176
100 DQV 0.4375 0.84
101 9ZD 0.436975 0.797468
102 8QN 0.436975 0.84
103 9ZA 0.436975 0.797468
104 T99 0.434783 0.772152
105 TAT 0.434783 0.772152
106 ANP 0.434783 0.782051
107 LAD 0.434426 0.8
108 KAA 0.434426 0.7
109 5N5 0.434343 0.828571
110 NSS 0.433333 0.704545
111 4AD 0.433333 0.807692
112 LSS 0.433333 0.688889
113 HQG 0.432203 0.815789
114 ME8 0.430894 0.780488
115 3OD 0.430894 0.828947
116 TXA 0.430894 0.818182
117 A4D 0.43 0.828571
118 APC MG 0.429825 0.802632
119 AHX 0.429752 0.765432
120 7MD 0.429688 0.780488
121 DAL AMP 0.428571 0.84
122 DND 0.427481 0.842105
123 ALF ADP 0.42735 0.7625
124 ATF 0.42735 0.772152
125 DTA 0.427184 0.819444
126 A6D 0.42623 0.728395
127 OAD 0.42623 0.828947
128 BEF ADP 0.426087 0.802632
129 AMP DBH 0.425197 0.853333
130 5SV 0.425 0.743902
131 5X8 0.424779 0.84507
132 TYM 0.424242 0.842105
133 WSA 0.424242 0.732558
134 SMM 0.423729 0.775
135 6YZ 0.423729 0.782051
136 MTA 0.423077 0.805556
137 P5A 0.422764 0.692308
138 R2V 0.422764 0.729412
139 A3R 0.421488 0.753086
140 ADQ 0.421488 0.828947
141 8Q2 0.421053 0.719101
142 DZD 0.42029 0.777778
143 NB8 0.419355 0.7875
144 K2R 0.419355 0.815789
145 PTJ 0.419355 0.7875
146 EP4 0.417476 0.783784
147 MAP 0.416667 0.7625
148 A22 0.416667 0.815789
149 NAX 0.416667 0.790123
150 MYR AMP 0.416 0.780488
151 KB1 0.416 0.815789
152 KXW 0.415385 0.826667
153 TAD 0.415385 0.756098
154 ANP MG 0.415254 0.792208
155 3DH 0.415094 0.805556
156 LEU LMS 0.414634 0.696629
157 9X8 0.414634 0.78481
158 A3P 0.414414 0.8
159 4UV 0.414062 0.831169
160 SAI 0.413793 0.835616
161 M2T 0.413462 0.763158
162 OZV 0.413223 0.802632
163 25A 0.413223 0.826667
164 SFG 0.412281 0.857143
165 LAQ 0.412214 0.780488
166 7C5 0.410853 0.902778
167 7MC 0.410448 0.761905
168 A1R 0.409836 0.753086
169 ATP A A A 0.409449 0.837838
170 K3K 0.409449 0.861111
171 ATP A 0.409449 0.837838
172 48N 0.409091 0.7875
173 M24 0.408451 0.8125
174 4UU 0.407692 0.831169
175 JNT 0.406504 0.782051
176 XAH 0.40625 0.759036
177 NAI 0.406015 0.797468
178 6V0 0.406015 0.7875
179 SA8 0.405172 0.802632
180 KY5 0.404762 0.8
181 SLU 0.404255 0.735632
182 6RE 0.40367 0.766234
183 K3E 0.403101 0.849315
184 NWW 0.401961 0.794118
185 MAO 0.401786 0.743902
186 SAH 0.401709 0.847222
187 AHZ 0.401515 0.802469
188 YLB 0.4 0.761905
189 L3W 0.4 0.794872
Similar Ligands (3D)
Ligand no: 1; Ligand: KOY; Similar ligands found: 0
No: Ligand Similarity coefficient
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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