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 MORE than expected: % Diff = 2;
submit data
475.35 C15 H22 N7 O9 P c1nc(...
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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 319 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 271 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 223 families.
1 6EC8 - J4G C15 H22 N7 O9 P c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: J4G; Similar ligands found: 249
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 AMP 0.549451 0.918919
8 A 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 V2G 0.519608 0.923077
14 XAH 0.508929 0.888889
15 A2P 0.505155 0.905405
16 CA0 0.50505 0.921053
17 AMO 0.504673 0.96
18 KG4 0.5 0.921053
19 AHX 0.5 0.898734
20 SRP 0.495238 0.96
21 WAQ 0.490909 0.935065
22 DSZ 0.490741 0.825581
23 5AL 0.490385 0.933333
24 NB8 0.486486 0.923077
25 QA7 0.485981 0.897436
26 5X8 0.485149 0.815789
27 ADP 0.484848 0.92
28 A2D 0.484536 0.894737
29 45A 0.484536 0.87013
30 ABM 0.484536 0.87013
31 7MD 0.482759 0.9125
32 SSA 0.481132 0.804598
33 V3L 0.480769 0.945946
34 SON 0.48 0.96
35 AN2 0.48 0.907895
36 OVE 0.479167 0.835443
37 AMP MG 0.479167 0.88
38 KAA 0.477477 0.797753
39 LAD 0.477477 0.935897
40 LSS 0.477064 0.786517
41 ADX 0.475248 0.809524
42 AU1 0.475248 0.896104
43 AP2 0.474747 0.909091
44 BA3 0.474747 0.894737
45 A12 0.474747 0.909091
46 3AM 0.473684 0.88
47 ME8 0.473214 0.9125
48 5CA 0.472222 0.804598
49 SAH 0.471154 0.818182
50 ACP 0.470588 0.921053
51 HEJ 0.470588 0.92
52 ATP 0.470588 0.92
53 2VA 0.470588 0.759494
54 AP5 0.47 0.894737
55 B4P 0.47 0.894737
56 9ZD 0.46789 0.910256
57 25A 0.46789 0.92
58 8QN 0.46789 0.933333
59 9ZA 0.46789 0.910256
60 8LH 0.46729 0.909091
61 ACQ 0.466667 0.921053
62 AQP 0.466019 0.92
63 5FA 0.466019 0.92
64 APC 0.466019 0.909091
65 AT4 0.465347 0.884615
66 7D3 0.464646 0.835443
67 F2R 0.464 0.91358
68 SRA 0.463918 0.871795
69 A1R 0.463636 0.886076
70 2AM 0.463158 0.868421
71 PPS 0.462264 0.809524
72 8LE 0.462264 0.897436
73 PAP 0.461538 0.906667
74 NVA 2AD 0.461538 0.7875
75 M33 0.460784 0.883117
76 TXA 0.460177 0.909091
77 FYA 0.460177 0.907895
78 PTJ 0.460177 0.898734
79 DA 0.459184 0.881579
80 D5M 0.459184 0.881579
81 YLB 0.459016 0.890244
82 8LQ 0.458716 0.934211
83 TSB 0.458716 0.781609
84 YLP 0.458333 0.890244
85 A5A 0.457944 0.790698
86 SO8 0.457143 0.75
87 YSA 0.456897 0.804598
88 50T 0.456311 0.883117
89 SFG 0.456311 0.826667
90 OOB 0.454545 0.933333
91 S7M 0.453704 0.759036
92 6YZ 0.453704 0.921053
93 ANP 0.45283 0.896104
94 T99 0.45283 0.884615
95 GAP 0.45283 0.896104
96 TAT 0.45283 0.884615
97 2A5 0.451923 0.896104
98 APR 0.451923 0.92
99 PRX 0.451923 0.871795
100 AR6 0.451923 0.92
101 J7V 0.451128 0.816092
102 ADP BEF 0.45098 0.893333
103 ADP MG 0.45098 0.893333
104 4AD 0.45045 0.947368
105 PAJ 0.45045 0.864198
106 HQG 0.449541 0.933333
107 VMS 0.449541 0.772727
108 54H 0.449541 0.772727
109 ADN 0.449438 0.776316
110 XYA 0.449438 0.776316
111 RAB 0.449438 0.776316
112 6RE 0.44898 0.7875
113 FA5 0.448276 0.96
114 AGS 0.447619 0.873418
115 AD9 0.447619 0.896104
116 SA8 0.447619 0.777778
117 RBY 0.447619 0.909091
118 ADV 0.447619 0.909091
119 ATR 0.447619 0.893333
120 1ZZ 0.447368 0.865854
121 YLC 0.447154 0.9125
122 7D4 0.446602 0.835443
123 DLL 0.446429 0.933333
124 48N 0.446281 0.898734
125 A22 0.445455 0.907895
126 DAL AMP 0.445455 0.907895
127 53H 0.445455 0.764045
128 ARG AMP 0.445378 0.901235
129 ATF 0.444444 0.884615
130 ALF ADP 0.444444 0.82716
131 ANP MG 0.444444 0.883117
132 SAI 0.443396 0.807692
133 OAD 0.442478 0.921053
134 IOT 0.44 0.902439
135 LMS 0.438776 0.788235
136 PR8 0.438596 0.924051
137 7D7 0.438202 0.705128
138 0UM 0.4375 0.768293
139 ADQ 0.4375 0.896104
140 SCO 0.437037 0.870588
141 CMX 0.437037 0.870588
142 YLA 0.436508 0.890244
143 52H 0.436364 0.764045
144 7MC 0.435484 0.890244
145 EEM 0.435185 0.759036
146 NWW 0.434783 0.72
147 5CD 0.434783 0.763158
148 ADP PO3 0.433962 0.893333
149 APC MG 0.433962 0.87013
150 ATP MG 0.433962 0.893333
151 NVA LMS 0.433628 0.797753
152 00A 0.433628 0.886076
153 JNT 0.433628 0.896104
154 AYB 0.433071 0.879518
155 MAP 0.432432 0.873418
156 DTA 0.431579 0.746835
157 VO4 ADP 0.431193 0.896104
158 KB1 0.431034 0.768293
159 MYR AMP 0.431034 0.843373
160 TM1 0.431034 0.758621
161 AOC 0.43 0.779221
162 BEF ADP 0.429907 0.87013
163 G5A 0.429907 0.804598
164 9X8 0.429825 0.873418
165 3UK 0.429825 0.921053
166 ADP BMA 0.429825 0.871795
167 5SV 0.428571 0.829268
168 9SN 0.42735 0.875
169 SMM 0.427273 0.752941
170 5AS 0.427184 0.744444
171 COD 0.426357 0.837209
172 B5V 0.426087 0.909091
173 SAM 0.425926 0.759036
174 J7C 0.425743 0.797468
175 NSS 0.424779 0.804598
176 5N5 0.423913 0.753247
177 B5M 0.423729 0.897436
178 A2R 0.423423 0.933333
179 3OD 0.422414 0.921053
180 GJV 0.421569 0.777778
181 ANZ 0.421488 0.761905
182 YLY 0.421053 0.879518
183 KYE 0.420168 0.783133
184 A4D 0.419355 0.753247
185 DND 0.419355 0.909091
186 25L 0.418803 0.907895
187 SCD 0.41844 0.870588
188 3DH 0.418367 0.734177
189 2SA 0.418182 0.96
190 AV2 0.418182 0.846154
191 COA 0.41791 0.848837
192 NA7 0.417391 0.909091
193 K15 0.417391 0.75
194 M2T 0.416667 0.698795
195 WSA 0.416 0.813953
196 OMR 0.416 0.855422
197 TYM 0.416 0.96
198 OZV 0.415929 0.894737
199 N5O 0.415842 0.792208
200 NEC 0.415842 0.708861
201 DAT 0.415094 0.883117
202 CUU 0.415094 0.92
203 HZ2 0.414634 0.780488
204 DCA 0.413534 0.848837
205 ETB 0.413534 0.858824
206 FCX 0.413043 0.840909
207 MTA 0.412371 0.734177
208 A3R 0.412281 0.886076
209 8PZ 0.411765 0.804598
210 B5Y 0.411765 0.897436
211 N0B 0.411765 0.890244
212 CMC 0.411348 0.850575
213 5AD 0.411111 0.706667
214 JB6 0.410256 0.886076
215 SXZ 0.410256 0.780488
216 A7D 0.409524 0.782051
217 80F 0.409091 0.86747
218 AMX 0.408759 0.858824
219 62X 0.408696 0.732558
220 LQJ 0.408333 0.87013
221 HY8 0.408 0.780488
222 N5A 0.407767 0.766234
223 0T1 0.407407 0.848837
224 8X1 0.40708 0.797753
225 GGZ 0.40708 0.764706
226 TAD 0.406504 0.864198
227 DQV 0.406504 0.907895
228 KXW 0.406504 0.777778
229 KH3 0.406504 0.741176
230 EP4 0.40625 0.716049
231 4UV 0.404959 0.897436
232 KGP 0.404255 0.752577
233 YZS 0.404255 0.752577
234 MCD 0.404255 0.850575
235 NWQ 0.40404 0.701299
236 GEK 0.403509 0.810127
237 LAQ 0.403226 0.865854
238 FAM 0.402878 0.829545
239 H1Q 0.401869 0.857143
240 P5A 0.401709 0.788889
241 L3W 0.401575 0.884615
242 WMP 0.401515 0.8
243 HAX 0.4 0.829545
244 SCA 0.4 0.850575
245 6IA 0.4 0.864198
246 ZZB 0.4 0.738636
247 DTP 0.4 0.883117
248 3AT 0.4 0.92
249 KMQ 0.4 0.884615
Similar Ligands (3D)
Ligand no: 1; Ligand: J4G; 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 : 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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