Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:501;
B:502;
B:501;
Part of Protein;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
4YB A:502;
B:503;
Valid;
Valid;
none;
none;
Kd = 394 nM
550.499 C21 H22 N6 O10 S 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: 4YB; Similar ligands found: 208
No: Ligand ECFP6 Tc MDL keys Tc
1 4YB 1 1
2 G5A 0.670103 0.931035
3 649 0.631579 0.932584
4 KOY 0.628319 0.767442
5 8PZ 0.623853 0.953488
6 B1U 0.618182 0.880435
7 A5A 0.617647 0.918605
8 DSZ 0.603774 0.953488
9 NVA LMS 0.598131 0.921348
10 SSA 0.596154 0.931035
11 54H 0.590476 0.897727
12 VMS 0.590476 0.897727
13 52H 0.590476 0.88764
14 GSU 0.587156 0.976471
15 8X1 0.584906 0.921348
16 53H 0.584906 0.88764
17 5CA 0.584906 0.931035
18 TSB 0.584906 0.908046
19 5AS 0.575758 0.866667
20 NSS 0.574074 0.931035
21 LSS 0.574074 0.910112
22 LMS 0.5625 0.917647
23 YSA 0.561404 0.953488
24 KAA 0.558559 0.921348
25 P5A 0.558559 0.911111
26 8Q2 0.558333 0.921348
27 WSA 0.53719 0.964706
28 QXP 0.522523 0.853933
29 3UK 0.522124 0.825581
30 SLU 0.507692 0.898876
31 SON 0.495238 0.795455
32 AMP MG 0.49505 0.747126
33 B5V 0.491379 0.816092
34 V2G 0.490909 0.788889
35 AOC 0.490196 0.681818
36 KG4 0.485981 0.784091
37 A 0.485149 0.758621
38 AMP 0.485149 0.758621
39 QXG 0.482759 0.844444
40 SRA 0.480392 0.784091
41 CA0 0.476636 0.784091
42 DLL 0.474138 0.813953
43 A2D 0.471154 0.781609
44 45A 0.471154 0.741573
45 ABM 0.471154 0.741573
46 LEU LMS 0.470085 0.857143
47 OOB 0.469565 0.813953
48 V47 0.469027 0.729412
49 GAP 0.468468 0.764045
50 S0N 0.466216 0.755102
51 R2V 0.466102 0.833333
52 8LE 0.464286 0.766667
53 AU1 0.462963 0.764045
54 M33 0.462963 0.752809
55 ADX 0.462963 0.873563
56 A12 0.462264 0.755556
57 BA3 0.462264 0.781609
58 AP2 0.462264 0.755556
59 TXA 0.462185 0.775281
60 8LQ 0.46087 0.795455
61 QA7 0.46087 0.766667
62 50T 0.458716 0.733333
63 5X8 0.458716 0.732558
64 H1Q 0.458716 0.75
65 AP5 0.457944 0.781609
66 B4P 0.457944 0.781609
67 ADP 0.457944 0.761364
68 PRX 0.454545 0.744444
69 9SN 0.454545 0.788889
70 APC 0.454545 0.755556
71 WAQ 0.453782 0.797753
72 AT4 0.453704 0.775281
73 ADP MG 0.453704 0.758621
74 ADP BEF 0.453704 0.758621
75 AN2 0.453704 0.772727
76 5CD 0.453608 0.666667
77 XYA 0.452632 0.678161
78 RAB 0.452632 0.678161
79 ADN 0.452632 0.678161
80 5AL 0.451327 0.793103
81 3DH 0.45098 0.662921
82 ADP PO3 0.45045 0.758621
83 ATP MG 0.45045 0.758621
84 AGS 0.45045 0.786517
85 1ZZ 0.45 0.744681
86 ALF ADP 0.447368 0.709677
87 67D 0.44697 0.954023
88 ATP 0.445455 0.761364
89 HEJ 0.445455 0.761364
90 ACP 0.445455 0.764045
91 9ZA 0.444444 0.777778
92 9ZD 0.444444 0.777778
93 AMP DBH 0.443548 0.764045
94 SRP 0.443478 0.816092
95 8LH 0.443478 0.775281
96 5N5 0.443299 0.659091
97 ANP 0.442478 0.764045
98 ACQ 0.442478 0.764045
99 APR 0.441441 0.781609
100 5FA 0.441441 0.761364
101 AQP 0.441441 0.761364
102 AR6 0.441441 0.781609
103 AMO 0.440678 0.816092
104 HQG 0.439655 0.772727
105 B5M 0.439024 0.806818
106 FA5 0.439024 0.837209
107 A4D 0.438776 0.678161
108 9K8 0.438017 0.8
109 NB8 0.438017 0.808989
110 594 0.437956 0.835052
111 AD9 0.4375 0.744444
112 APC MG 0.4375 0.741573
113 RBY 0.4375 0.775281
114 ADV 0.4375 0.775281
115 AHX 0.436975 0.788889
116 00A 0.436975 0.777778
117 7MD 0.436508 0.802198
118 DAL AMP 0.435897 0.772727
119 A22 0.435897 0.772727
120 DTA 0.435644 0.712644
121 ANP MG 0.434783 0.772727
122 MYR AMP 0.434426 0.726316
123 DND 0.434109 0.795455
124 BEF ADP 0.433628 0.741573
125 25A 0.432203 0.781609
126 8QN 0.432203 0.793103
127 MTA 0.431373 0.662921
128 J7C 0.429907 0.681319
129 TAT 0.429825 0.775281
130 T99 0.429825 0.775281
131 PR8 0.429752 0.791209
132 LAD 0.429752 0.8
133 PAJ 0.428571 0.741935
134 4AD 0.428571 0.806818
135 ADQ 0.428571 0.784091
136 YLB 0.427481 0.765957
137 B5Y 0.427419 0.806818
138 K3K 0.427419 0.688889
139 FYA 0.42623 0.793103
140 ME8 0.42623 0.802198
141 EP4 0.425743 0.630435
142 A5D 0.424779 0.712644
143 SA8 0.424779 0.684783
144 6RE 0.424528 0.673913
145 MAP 0.423729 0.747253
146 NAX 0.423077 0.791209
147 ATF 0.422414 0.736264
148 VO4 ADP 0.422414 0.744444
149 DQV 0.421875 0.793103
150 M2T 0.421569 0.652174
151 OAD 0.421488 0.784091
152 SAH 0.421053 0.735632
153 5SV 0.420168 0.712766
154 SFG 0.419643 0.72093
155 6YZ 0.418803 0.764045
156 LAQ 0.418605 0.782609
157 A3N 0.416667 0.637363
158 0UM 0.416667 0.677419
159 YLP 0.415385 0.765957
160 PTJ 0.414634 0.75
161 BIS 0.414634 0.73913
162 3OD 0.414634 0.784091
163 590 0.413793 0.845361
164 EEM 0.413793 0.670213
165 GJV 0.412844 0.666667
166 XAH 0.412698 0.782609
167 25L 0.41129 0.772727
168 KXW 0.410853 0.703297
169 TAD 0.410853 0.76087
170 NWW 0.41 0.627907
171 K15 0.409836 0.663158
172 9X8 0.409836 0.786517
173 ADP BMA 0.409836 0.764045
174 4UV 0.409449 0.786517
175 K3E 0.409449 0.681319
176 OMR 0.409091 0.736842
177 MAO 0.409091 0.712766
178 TYM 0.409091 0.837209
179 SAI 0.408696 0.707865
180 OZV 0.408333 0.761364
181 DSH 0.407407 0.681319
182 NEC 0.407407 0.622222
183 A3G 0.407407 0.704545
184 SMM 0.40678 0.702128
185 S7M 0.40678 0.706522
186 7C5 0.40625 0.741573
187 NAD IBO 0.406015 0.781609
188 7MC 0.406015 0.784946
189 NAD TDB 0.406015 0.781609
190 A1R 0.404959 0.758242
191 A3R 0.404959 0.758242
192 ATP A 0.404762 0.770115
193 ATP A A A 0.404762 0.770115
194 LPA AMP 0.40458 0.763441
195 48N 0.40458 0.769231
196 BS5 0.404412 0.802083
197 SXZ 0.403226 0.706522
198 ARG AMP 0.403101 0.755319
199 ZAS 0.401869 0.677778
200 JNT 0.401639 0.764045
201 EU9 0.401515 0.755319
202 6V0 0.401515 0.75
203 F2R 0.40146 0.765957
204 S4M 0.4 0.649485
205 KY5 0.4 0.681319
206 IOT 0.4 0.757895
207 KB1 0.4 0.695652
208 EO7 0.4 0.876405
Similar Ligands (3D)
Ligand no: 1; Ligand: 4YB; 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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