Receptor
PDB id Resolution Class Description Source Keywords
6EC8 2.15 Å EC: 7.-.-.- GLUTAMYLATION DOMAIN, TBTB, FROM THIOMURACIN BIOSYNTHESIS BO PHOSPHODESMETHYLGLUTAMYCIN THERMOBISPORA BISPORA (STRAIN ATCC 19943833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) RIPP THIOPEPTIDE THIOMURACIN TRNA-DEPENDENT GLUTAMYLATIODEHYDRATASE BIOSYNTHETIC PROTEIN
Ref.: CHARACTERIZATION OF GLUTAMYL-TRNA-DEPENDENT DEHYDRA USING NONREACTIVE SUBSTRATE MIMICS. PROC.NATL.ACAD.SCI.USA V. 116 17245 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
J4G A:901;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data
475.35 C15 H22 N7 O9 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6EC8 2.15 Å EC: 7.-.-.- GLUTAMYLATION DOMAIN, TBTB, FROM THIOMURACIN BIOSYNTHESIS BO PHOSPHODESMETHYLGLUTAMYCIN THERMOBISPORA BISPORA (STRAIN ATCC 19943833 / CBS 139.67 / JCM 10125 / NBRC 14880 / R51) RIPP THIOPEPTIDE THIOMURACIN TRNA-DEPENDENT GLUTAMYLATIODEHYDRATASE BIOSYNTHETIC PROTEIN
Ref.: CHARACTERIZATION OF GLUTAMYL-TRNA-DEPENDENT DEHYDRA USING NONREACTIVE SUBSTRATE MIMICS. PROC.NATL.ACAD.SCI.USA V. 116 17245 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 6EC8 - J4G C15 H22 N7 O9 P c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 6EC8 - J4G C15 H22 N7 O9 P c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 6EC8 - J4G C15 H22 N7 O9 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: J4G; Similar ligands found: 243
No: Ligand ECFP6 Tc MDL keys Tc
1 J4G 1 1
2 A3S 0.626374 0.815789
3 GSU 0.592233 0.847059
4 D3Y 0.574257 0.794872
5 A3T 0.5625 0.779221
6 3NZ 0.561905 0.7875
7 A 0.549451 0.918919
8 AMP 0.549451 0.918919
9 A3G 0.537634 0.805195
10 7D5 0.533333 0.833333
11 VRT 0.53 0.797468
12 A3P 0.520833 0.918919
13 XAH 0.508929 0.888889
14 A2P 0.505155 0.905405
15 CA0 0.50505 0.921053
16 AMO 0.504673 0.96
17 AHX 0.5 0.898734
18 KG4 0.5 0.921053
19 SRP 0.495238 0.96
20 WAQ 0.490909 0.935065
21 DSZ 0.490741 0.825581
22 5AL 0.490385 0.933333
23 NB8 0.486486 0.923077
24 5X8 0.485149 0.815789
25 ADP 0.484848 0.92
26 A2D 0.484536 0.894737
27 45A 0.484536 0.87013
28 ABM 0.484536 0.87013
29 7MD 0.482759 0.9125
30 SSA 0.481132 0.804598
31 V3L 0.480769 0.945946
32 AN2 0.48 0.907895
33 SON 0.48 0.96
34 OVE 0.479167 0.835443
35 LAD 0.477477 0.935897
36 KAA 0.477477 0.797753
37 LSS 0.477064 0.786517
38 AU1 0.475248 0.896104
39 ADX 0.475248 0.809524
40 A12 0.474747 0.909091
41 AP2 0.474747 0.909091
42 BA3 0.474747 0.894737
43 3AM 0.473684 0.88
44 ME8 0.473214 0.9125
45 5CA 0.472222 0.804598
46 SAH 0.471154 0.818182
47 2VA 0.470588 0.759494
48 ACP 0.470588 0.921053
49 HEJ 0.470588 0.92
50 ATP 0.470588 0.92
51 B4P 0.47 0.894737
52 AP5 0.47 0.894737
53 9ZA 0.46789 0.910256
54 25A 0.46789 0.92
55 9ZD 0.46789 0.910256
56 8QN 0.46789 0.933333
57 8LH 0.46729 0.909091
58 ACQ 0.466667 0.921053
59 APC 0.466019 0.909091
60 AQP 0.466019 0.92
61 5FA 0.466019 0.92
62 AT4 0.465347 0.884615
63 7D3 0.464646 0.835443
64 F2R 0.464 0.91358
65 SRA 0.463918 0.871795
66 A1R 0.463636 0.886076
67 2AM 0.463158 0.868421
68 PPS 0.462264 0.809524
69 8LE 0.462264 0.897436
70 NVA 2AD 0.461538 0.7875
71 PAP 0.461538 0.906667
72 YAP 0.46087 0.947368
73 M33 0.460784 0.883117
74 FYA 0.460177 0.907895
75 PTJ 0.460177 0.898734
76 TXA 0.460177 0.909091
77 D5M 0.459184 0.881579
78 DA 0.459184 0.881579
79 YLB 0.459016 0.890244
80 TSB 0.458716 0.781609
81 8LQ 0.458716 0.934211
82 YLP 0.458333 0.890244
83 A5A 0.457944 0.790698
84 SO8 0.457143 0.75
85 YSA 0.456897 0.804598
86 50T 0.456311 0.883117
87 SFG 0.456311 0.826667
88 OOB 0.454545 0.933333
89 S7M 0.453704 0.759036
90 6YZ 0.453704 0.921053
91 GAP 0.45283 0.896104
92 ANP 0.45283 0.896104
93 T99 0.45283 0.884615
94 TAT 0.45283 0.884615
95 PRX 0.451923 0.871795
96 APR 0.451923 0.92
97 2A5 0.451923 0.896104
98 AR6 0.451923 0.92
99 J7V 0.451128 0.816092
100 ADP MG 0.45098 0.893333
101 PAJ 0.45045 0.864198
102 4AD 0.45045 0.947368
103 HQG 0.449541 0.933333
104 54H 0.449541 0.772727
105 VMS 0.449541 0.772727
106 ADN 0.449438 0.776316
107 RAB 0.449438 0.776316
108 XYA 0.449438 0.776316
109 6RE 0.44898 0.7875
110 FA5 0.448276 0.96
111 AD9 0.447619 0.896104
112 ATR 0.447619 0.893333
113 SAP 0.447619 0.873418
114 ADV 0.447619 0.909091
115 RBY 0.447619 0.909091
116 AGS 0.447619 0.873418
117 SA8 0.447619 0.777778
118 1ZZ 0.447368 0.865854
119 YLC 0.447154 0.9125
120 7D4 0.446602 0.835443
121 DLL 0.446429 0.933333
122 48N 0.446281 0.898734
123 53H 0.445455 0.764045
124 DAL AMP 0.445455 0.907895
125 A22 0.445455 0.907895
126 ARG AMP 0.445378 0.901235
127 ALF ADP 0.444444 0.82716
128 ADP ALF 0.444444 0.82716
129 ATF 0.444444 0.884615
130 SAI 0.443396 0.807692
131 OAD 0.442478 0.921053
132 IOT 0.44 0.902439
133 LMS 0.438776 0.788235
134 PR8 0.438596 0.924051
135 7D7 0.438202 0.705128
136 ADQ 0.4375 0.896104
137 0UM 0.4375 0.768293
138 SCO 0.437037 0.870588
139 CMX 0.437037 0.870588
140 YLA 0.436508 0.890244
141 52H 0.436364 0.764045
142 7MC 0.435484 0.890244
143 EEM 0.435185 0.759036
144 5CD 0.434783 0.763158
145 APC MG 0.433962 0.87013
146 ADP PO3 0.433962 0.893333
147 ATP MG 0.433962 0.893333
148 00A 0.433628 0.886076
149 NVA LMS 0.433628 0.797753
150 AYB 0.433071 0.879518
151 MAP 0.432432 0.873418
152 DTA 0.431579 0.746835
153 KB1 0.431034 0.768293
154 TM1 0.431034 0.758621
155 MYR AMP 0.431034 0.843373
156 AOC 0.43 0.779221
157 G5A 0.429907 0.804598
158 3UK 0.429825 0.921053
159 9X8 0.429825 0.873418
160 ADP BMA 0.429825 0.871795
161 5SV 0.428571 0.829268
162 9SN 0.42735 0.875
163 SMM 0.427273 0.752941
164 5AS 0.427184 0.744444
165 COD 0.426357 0.837209
166 B5V 0.426087 0.909091
167 SAM 0.425926 0.759036
168 J7C 0.425743 0.797468
169 NSS 0.424779 0.804598
170 5N5 0.423913 0.753247
171 B5M 0.423729 0.897436
172 A2R 0.423423 0.933333
173 3OD 0.422414 0.921053
174 GJV 0.421569 0.777778
175 ANZ 0.421488 0.761905
176 YLY 0.421053 0.879518
177 A4D 0.419355 0.753247
178 DND 0.419355 0.909091
179 NXX 0.419355 0.909091
180 25L 0.418803 0.907895
181 SCD 0.41844 0.870588
182 3DH 0.418367 0.734177
183 2SA 0.418182 0.96
184 AV2 0.418182 0.846154
185 COA 0.41791 0.848837
186 LEU LMS 0.417391 0.777778
187 K15 0.417391 0.75
188 NA7 0.417391 0.909091
189 M2T 0.416667 0.698795
190 TYR AMP 0.416667 0.922078
191 WSA 0.416 0.813953
192 OMR 0.416 0.855422
193 TYM 0.416 0.96
194 OZV 0.415929 0.894737
195 N5O 0.415842 0.792208
196 NEC 0.415842 0.708861
197 DAT 0.415094 0.883117
198 HZ2 0.414634 0.780488
199 ADP VO4 0.414414 0.883117
200 VO4 ADP 0.414414 0.883117
201 ETB 0.413534 0.858824
202 DCA 0.413534 0.848837
203 FCX 0.413043 0.840909
204 MTA 0.412371 0.734177
205 A3R 0.412281 0.886076
206 N0B 0.411765 0.890244
207 B5Y 0.411765 0.897436
208 8PZ 0.411765 0.804598
209 CMC 0.411348 0.850575
210 5AD 0.411111 0.706667
211 JB6 0.410256 0.886076
212 SXZ 0.410256 0.780488
213 A7D 0.409524 0.782051
214 80F 0.409091 0.86747
215 AMX 0.408759 0.858824
216 62X 0.408696 0.732558
217 LQJ 0.408333 0.87013
218 HY8 0.408 0.780488
219 N5A 0.407767 0.766234
220 0T1 0.407407 0.848837
221 GGZ 0.40708 0.764706
222 8X1 0.40708 0.797753
223 DQV 0.406504 0.907895
224 TAD 0.406504 0.864198
225 KH3 0.406504 0.741176
226 EP4 0.40625 0.716049
227 A A A 0.405172 0.883117
228 4UV 0.404959 0.897436
229 KGP 0.404255 0.752577
230 YZS 0.404255 0.752577
231 MCD 0.404255 0.850575
232 GEK 0.403509 0.810127
233 LAQ 0.403226 0.865854
234 FAM 0.402878 0.829545
235 H1Q 0.401869 0.857143
236 P5A 0.401709 0.788889
237 WMP 0.401515 0.8
238 DTP 0.4 0.883117
239 ZZB 0.4 0.738636
240 SCA 0.4 0.850575
241 HAX 0.4 0.829545
242 3AT 0.4 0.92
243 6IA 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6EC8; Ligand: J4G; 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: 6ec8.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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