Receptor
PDB id Resolution Class Description Source Keywords
6E3A 1.4 Å EC: 2.7.1.- TRNA 2'-PHOSPHOTRANSFERASE CLOSTRIDIUM THERMOCELLUM (STRAIN ATCC DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 73ORGANISM_COMMON: RUMINICLOSTRIDIUM THERMOCELLUM KPTA TPT1 TRPT1 TRANSFERASE
Ref.: STRUCTURE OF TRNA SPLICING ENZYME TPT1 ILLUMINATES MECHANISM OF RNA 2'-PO4RECOGNITION AND ADP-RIBOSYLA NAT COMMUN V. 10 218 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HQG A:202;
Valid;
none;
submit data
639.296 C15 H24 N5 O17 P3 c1nc(...
COA A:201;
Invalid;
none;
submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6E3A 1.4 Å EC: 2.7.1.- TRNA 2'-PHOSPHOTRANSFERASE CLOSTRIDIUM THERMOCELLUM (STRAIN ATCC DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 73ORGANISM_COMMON: RUMINICLOSTRIDIUM THERMOCELLUM KPTA TPT1 TRPT1 TRANSFERASE
Ref.: STRUCTURE OF TRNA SPLICING ENZYME TPT1 ILLUMINATES MECHANISM OF RNA 2'-PO4RECOGNITION AND ADP-RIBOSYLA NAT COMMUN V. 10 218 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 6E3A - HQG C15 H24 N5 O17 P3 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6E3A - HQG C15 H24 N5 O17 P3 c1nc(c2c(n....
2 6EDE - HQG C15 H24 N5 O17 P3 c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6E3A - HQG C15 H24 N5 O17 P3 c1nc(c2c(n....
2 6EDE - HQG C15 H24 N5 O17 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: HQG; Similar ligands found: 455
No: Ligand ECFP6 Tc MDL keys Tc
1 HQG 1 1
2 A2D 0.815789 0.958333
3 BA3 0.772152 0.958333
4 AP5 0.7625 0.958333
5 ADP 0.7625 0.985915
6 B4P 0.7625 0.958333
7 ADQ 0.761364 0.958904
8 AGS 0.759036 0.933333
9 ATP 0.756098 0.985915
10 HEJ 0.756098 0.985915
11 AR6 0.746988 0.985915
12 AQP 0.746988 0.985915
13 5FA 0.746988 0.985915
14 APR 0.746988 0.985915
15 A22 0.738636 0.972222
16 AT4 0.731707 0.945946
17 AN2 0.731707 0.972222
18 M33 0.722892 0.945205
19 AD9 0.717647 0.958904
20 ACP 0.714286 0.958904
21 AMP 0.708861 0.957747
22 A 0.708861 0.957747
23 ATF 0.704545 0.945946
24 ACQ 0.701149 0.958904
25 CA0 0.682353 0.958904
26 ADX 0.682353 0.8625
27 ANP 0.681818 0.958904
28 SRA 0.679012 0.906667
29 6YZ 0.677778 0.958904
30 JNT 0.677419 0.932432
31 50T 0.674419 0.945205
32 KG4 0.674419 0.958904
33 PRX 0.666667 0.881579
34 A3R 0.666667 0.896104
35 A1R 0.666667 0.896104
36 45A 0.662651 0.905405
37 ABM 0.662651 0.905405
38 AMP MG 0.658537 0.916667
39 OAD 0.652632 0.958904
40 9X8 0.652632 0.933333
41 25L 0.649485 0.972222
42 APC 0.647727 0.945946
43 AP2 0.647059 0.945946
44 A12 0.647059 0.945946
45 TAT 0.644444 0.945946
46 T99 0.644444 0.945946
47 3OD 0.639175 0.958904
48 25A 0.638298 0.958333
49 8LE 0.637363 0.907895
50 5AL 0.637363 0.945205
51 ADP BMA 0.635417 0.932432
52 ADP BEF 0.632184 0.930556
53 ADP MG 0.632184 0.930556
54 00A 0.625 0.896104
55 AU1 0.625 0.958904
56 SRP 0.623656 0.92
57 8LH 0.623656 0.92
58 BIS 0.622449 0.921053
59 KMQ 0.62 0.945946
60 4AD 0.614583 0.933333
61 AFH 0.61165 0.897436
62 8LQ 0.610526 0.92
63 QA7 0.610526 0.907895
64 ADV 0.604396 0.945946
65 RBY 0.604396 0.945946
66 APC MG 0.604396 0.905405
67 ATP MG 0.604396 0.930556
68 ADP PO3 0.604396 0.930556
69 8QN 0.604167 0.945205
70 5SV 0.604167 0.8375
71 OOB 0.604167 0.945205
72 OZV 0.604167 0.958333
73 6V0 0.603774 0.884615
74 A2R 0.6 1
75 PAJ 0.597938 0.897436
76 AMO 0.597938 0.945946
77 BEF ADP 0.597826 0.905405
78 LAD 0.59596 0.873418
79 VO4 ADP 0.595745 0.932432
80 AHX 0.591837 0.884615
81 DLL 0.591837 0.945205
82 DQV 0.590476 0.945205
83 TXA 0.59 0.945946
84 ME8 0.59 0.851852
85 PTJ 0.59 0.909091
86 NB8 0.59 0.909091
87 NAX 0.588785 0.8625
88 ATR 0.586957 0.957747
89 PAP 0.586957 0.971831
90 G3A 0.586538 0.909091
91 3UK 0.585859 0.932432
92 V2G 0.585106 0.909091
93 G5P 0.580952 0.909091
94 F2R 0.580357 0.876543
95 PR8 0.58 0.8625
96 B5V 0.58 0.92
97 WAQ 0.58 0.896104
98 48N 0.579439 0.909091
99 ALF ADP 0.578947 0.858974
100 ANP MG 0.578947 0.918919
101 AP0 0.577982 0.884615
102 L3W 0.577982 0.92
103 SON 0.577778 0.945946
104 MAP 0.57732 0.933333
105 139 0.576577 0.8625
106 GTA 0.575472 0.875
107 GAP 0.574468 0.906667
108 FYA 0.574257 0.893333
109 1ZZ 0.574257 0.851852
110 TXD 0.574074 0.896104
111 UP5 0.574074 0.907895
112 NAI 0.574074 0.896104
113 DND 0.574074 0.945946
114 ITT 0.571429 0.930556
115 LMS 0.569767 0.817073
116 TXE 0.568807 0.896104
117 OMR 0.568807 0.864198
118 XAH 0.567308 0.829268
119 AR6 AR6 0.566038 0.931507
120 9SN 0.563107 0.884615
121 DAL AMP 0.561224 0.918919
122 2A5 0.55914 0.906667
123 V3L 0.557895 0.985915
124 B5Y 0.557692 0.907895
125 FA5 0.557692 0.92
126 B5M 0.557692 0.907895
127 XYA 0.556962 0.833333
128 RAB 0.556962 0.833333
129 ADN 0.556962 0.833333
130 A3P 0.555556 0.957747
131 9ZA 0.555556 0.921053
132 9ZD 0.555556 0.921053
133 NA7 0.554455 0.945946
134 7D4 0.554348 0.893333
135 80F 0.551724 0.853659
136 4TC 0.54955 0.884615
137 UPA 0.54955 0.896104
138 ADJ 0.548673 0.864198
139 T5A 0.548673 0.831325
140 COD 0.547826 0.802326
141 4UV 0.54717 0.907895
142 A4P 0.544643 0.833333
143 7D3 0.544444 0.893333
144 CNA 0.54386 0.92
145 5N5 0.54321 0.808219
146 LAQ 0.541284 0.851852
147 3AM 0.54023 0.916667
148 AOC 0.539326 0.810811
149 A2P 0.538462 0.943662
150 4UU 0.537037 0.907895
151 GA7 0.537037 0.894737
152 YLP 0.536364 0.831325
153 PPS 0.536082 0.8625
154 5AS 0.532609 0.770115
155 4UW 0.531532 0.873418
156 HFD 0.53125 0.933333
157 JSQ 0.53125 0.933333
158 G5A 0.53125 0.770115
159 ATP A A A 0.528302 0.917808
160 ATP A 0.528302 0.917808
161 YLB 0.522124 0.831325
162 TAD 0.518182 0.873418
163 A4D 0.518072 0.808219
164 5CD 0.518072 0.794521
165 EP4 0.517647 0.74359
166 7D5 0.517241 0.866667
167 JB6 0.514286 0.871795
168 RGT 0.514019 0.972603
169 TYM 0.513274 0.92
170 2AM 0.511364 0.930556
171 MYR AMP 0.509434 0.829268
172 ARG AMP 0.509091 0.841463
173 YLC 0.508772 0.851852
174 NAD 0.508475 0.918919
175 MTA 0.505747 0.763158
176 6AD 0.50505 0.897436
177 EAD 0.504 0.8625
178 IOT 0.5 0.843373
179 H1Q 0.5 0.891892
180 A3D 0.5 0.906667
181 NJP 0.5 0.933333
182 ODP 0.5 0.897436
183 BTX 0.495798 0.831325
184 0WD 0.495798 0.909091
185 YLA 0.495726 0.831325
186 NPW 0.495726 0.875
187 7MD 0.495495 0.875
188 AVV 0.495146 0.884615
189 3AT 0.494949 0.958333
190 6RE 0.494505 0.75
191 3DH 0.494382 0.763158
192 M2T 0.494253 0.725
193 DTA 0.494253 0.776316
194 BT5 0.491667 0.843373
195 AYB 0.491525 0.821429
196 AMP DBH 0.490909 0.906667
197 NO7 0.490196 0.92
198 A3G 0.48913 0.789474
199 P1H 0.488372 0.841463
200 AHZ 0.486726 0.829268
201 TSB 0.485437 0.809524
202 AV2 0.485149 0.905405
203 A5A 0.485149 0.797619
204 CUU 0.484536 0.958333
205 IMO 0.483871 0.916667
206 NAE 0.483871 0.883117
207 ZAS 0.483516 0.75641
208 NDP 0.483051 0.909091
209 LPA AMP 0.482456 0.829268
210 FB0 0.480916 0.795455
211 SSA 0.480392 0.790698
212 DTP 0.48 0.893333
213 NAQ 0.48 0.860759
214 DZD 0.479339 0.873418
215 NZQ 0.478992 0.897436
216 TXP 0.478992 0.909091
217 S4M 0.478723 0.659091
218 6MZ 0.478723 0.917808
219 OVE 0.478261 0.893333
220 ZID 0.47619 0.906667
221 NSS 0.47619 0.790698
222 38V 0.47619 0.875
223 LSS 0.47619 0.752809
224 M24 0.475806 0.8625
225 VMS 0.475728 0.77907
226 54H 0.475728 0.77907
227 52H 0.475728 0.770115
228 AF3 ADP 3PG 0.474138 0.85
229 ALF ADP 3PG 0.474138 0.85
230 SFD 0.474074 0.726316
231 FDA 0.473684 0.823529
232 DSH 0.473118 0.716049
233 D4F 0.472 0.851852
234 ARU 0.471698 0.85
235 NVA LMS 0.471698 0.744444
236 NAJ PZO 0.471545 0.8375
237 5CA 0.471154 0.790698
238 8X1 0.471154 0.744444
239 53H 0.471154 0.770115
240 6FA 0.470149 0.831325
241 7MC 0.470085 0.853659
242 NAD TDB 0.470085 0.905405
243 NAD IBO 0.470085 0.905405
244 DAT 0.469388 0.893333
245 5X8 0.469388 0.776316
246 J7C 0.468085 0.759494
247 A3N 0.468085 0.776316
248 ETB 0.467742 0.823529
249 DCA 0.467742 0.813953
250 LEU LMS 0.46729 0.741573
251 NDE 0.465649 0.92
252 YLY 0.464 0.821429
253 FAS 0.463235 0.841463
254 FAD 0.463235 0.841463
255 GJV 0.463158 0.740741
256 KAA 0.462963 0.744444
257 P5A 0.462963 0.736264
258 DSZ 0.462264 0.811765
259 62F 0.460432 0.851852
260 COA 0.460317 0.813953
261 0T1 0.460317 0.813953
262 XNP 0.459016 0.8625
263 4TA 0.459016 0.797619
264 9K8 0.458716 0.725275
265 71V 0.458333 0.896104
266 MAO 0.458333 0.75
267 SCO 0.457364 0.835294
268 O02 0.455446 0.909091
269 SAH 0.455446 0.75641
270 LQJ 0.455357 0.905405
271 GKE 0.455357 0.897436
272 GDC 0.455357 0.897436
273 GDD 0.455357 0.897436
274 SFG 0.454545 0.763158
275 N0B 0.453125 0.831325
276 PUA 0.452381 0.873418
277 V1N 0.451327 0.931507
278 DDS 0.45098 0.866667
279 7DT 0.45 0.971831
280 AMX 0.449612 0.823529
281 30N 0.449612 0.744681
282 COS 0.449612 0.795455
283 CAO 0.449612 0.786517
284 J4G 0.449541 0.933333
285 GSU 0.449541 0.790698
286 7DD 0.44898 0.971831
287 NWW 0.448276 0.75
288 NDC 0.447761 0.860759
289 AMP NAD 0.447154 0.918919
290 FAY 0.446809 0.851852
291 K3K 0.446429 0.792208
292 8PZ 0.446429 0.790698
293 CMX 0.446154 0.835294
294 SA8 0.445545 0.719512
295 NAJ PYZ 0.445312 0.797619
296 PGS 0.444444 0.871795
297 RFL 0.443662 0.811765
298 OXK 0.443609 0.816092
299 ACO 0.442748 0.786517
300 FCX 0.442748 0.806818
301 FAM 0.442748 0.795455
302 YSA 0.442478 0.770115
303 APU 0.441667 0.883117
304 SAI 0.441176 0.746835
305 6C6 0.441176 0.87013
306 5AD 0.440476 0.736111
307 PO4 PO4 A A A A PO4 0.440367 0.890411
308 CO6 0.440298 0.795455
309 FNK 0.439716 0.795455
310 4YB 0.439655 0.772727
311 HAX 0.439394 0.795455
312 K3E 0.438596 0.782051
313 DG1 0.438462 0.909091
314 Z5A 0.438462 0.770115
315 1DG 0.438462 0.909091
316 YXS 0.437956 0.721649
317 YXR 0.437956 0.721649
318 2MC 0.437037 0.76087
319 6IA 0.436893 0.82716
320 Y3J 0.436782 0.716216
321 3KK 0.43609 0.795455
322 FYN 0.43609 0.813953
323 7D7 0.435294 0.733333
324 7L1 0.435115 0.786517
325 1GZ 0.434783 0.786517
326 A3S 0.434343 0.8
327 A7D 0.434343 0.766234
328 CA6 0.432836 0.721649
329 YZS 0.432836 0.721649
330 SOP 0.432836 0.795455
331 COK 0.432836 0.795455
332 KGP 0.432836 0.721649
333 MCD 0.432836 0.816092
334 AAT 0.432692 0.698795
335 EEM 0.432692 0.702381
336 KOY 0.432203 0.815789
337 101 0.431579 0.866667
338 9JJ 0.431507 0.851852
339 A5D 0.431373 0.776316
340 N6P 0.431193 0.902778
341 NAP 0.430769 0.932432
342 COO 0.430657 0.795455
343 MCA 0.430657 0.806818
344 MHZ 0.43 0.689655
345 GGZ 0.429907 0.814815
346 B1U 0.429825 0.728261
347 CMC 0.42963 0.816092
348 NMX 0.42963 0.752688
349 1VU 0.42963 0.786517
350 128 0.428571 0.788235
351 2SA 0.428571 0.945946
352 TAP 0.427481 0.896104
353 DA 0.427083 0.866667
354 NEC 0.427083 0.736842
355 D5M 0.427083 0.866667
356 AIR 0.426966 0.888889
357 SCD 0.426471 0.835294
358 CAJ 0.426471 0.816092
359 GEK 0.425926 0.75
360 649 0.425 0.736264
361 S7M 0.424528 0.702381
362 SMM 0.424528 0.697674
363 KGA 0.42446 0.755319
364 IRC 0.42446 0.804598
365 NA0 0.424242 0.92
366 KL2 0.423913 0.826667
367 3HC 0.423358 0.804598
368 KGJ 0.423358 0.744681
369 MLC 0.423358 0.816092
370 BCO 0.423358 0.795455
371 1HE 0.423358 0.777778
372 IVC 0.423358 0.804598
373 A1S 0.423358 0.795455
374 SAM 0.423077 0.702381
375 AAM 0.42268 0.957747
376 7C5 0.422414 0.831169
377 8Q2 0.421488 0.764045
378 4CA 0.421429 0.786517
379 SO5 0.42029 0.731959
380 LCV 0.42029 0.731959
381 YE1 0.42029 0.804598
382 CAA 0.42029 0.804598
383 CO7 0.42029 0.795455
384 C2R 0.419355 0.917808
385 AMZ 0.419355 0.90411
386 SCA 0.417266 0.816092
387 MC4 0.417266 0.752688
388 2CP 0.417266 0.806818
389 FA9 0.417219 0.853659
390 GSP 0.416667 0.8625
391 P5F 0.416107 0.835294
392 9BG 0.416 0.884615
393 A6D 0.414414 0.714286
394 3CP 0.414286 0.816092
395 HGG 0.414286 0.816092
396 BYC 0.414286 0.795455
397 KFV 0.414286 0.729167
398 COF 0.414286 0.777778
399 CA8 0.414286 0.721649
400 2KQ 0.414286 0.797753
401 COW 0.414286 0.786517
402 GP3 0.413462 0.909091
403 WSA 0.413223 0.77907
404 QXP 0.412844 0.776471
405 6K6 0.412844 0.917808
406 1CZ 0.412587 0.806818
407 S0N 0.412587 0.816092
408 FAJ 0.411765 0.821429
409 A3T 0.411765 0.810811
410 12D 0.411765 0.797619
411 FAQ 0.411348 0.795455
412 BCA 0.411348 0.786517
413 V47 0.411215 0.797297
414 GTP 0.411215 0.907895
415 F2N 0.410596 0.804598
416 NIA 0.410526 0.8125
417 GDP 0.409524 0.907895
418 0UM 0.409091 0.710843
419 GRA 0.408451 0.816092
420 HXC 0.408451 0.777778
421 AS 0.408163 0.822785
422 G1R 0.407407 0.921053
423 JB3 0.406504 0.886076
424 TGC 0.405594 0.806818
425 62X 0.405405 0.678161
426 K2H 0.405405 0.746835
427 K2W 0.405172 0.731707
428 WCA 0.40411 0.777778
429 N5A 0.40404 0.727273
430 NVA 2AD 0.403846 0.75
431 KY2 0.40367 0.722892
432 KY5 0.403509 0.716049
433 PLP AAD 0.403101 0.725275
434 CIC 0.402778 0.816092
435 N9V 0.402778 0.806818
436 CO8 0.402778 0.777778
437 2NE 0.402778 0.777778
438 HDV 0.401869 0.881579
439 QXG 0.401786 0.767442
440 K15 0.401786 0.694118
441 GFB 0.401709 0.897436
442 GDR 0.401709 0.897436
443 NHD 0.401575 0.893333
444 4KX 0.401361 0.769231
445 MFK 0.4 0.777778
446 5F9 0.4 0.777778
447 NWQ 0.4 0.72973
448 4CO 0.4 0.786517
449 DCC 0.4 0.777778
450 K38 0.4 0.769231
451 UCC 0.4 0.777778
452 ST9 0.4 0.777778
453 S8M 0.4 0.75
454 0FQ 0.4 0.795455
455 MYA 0.4 0.777778
Similar Ligands (3D)
Ligand no: 1; Ligand: HQG; 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 : 6E3A; Ligand: HQG; 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: 6e3a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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