Receptor
PDB id Resolution Class Description Source Keywords
2GA9 2.3 Å EC: 2.1.1.57 CRYSTAL STRUCTURE OF THE HETERODIMERIC VACCINIA VIRUS POLYAD POLYMERASE WITH BOUND ATP-GAMMA-S VACCINIA VIRUS POLYADENYLATE POLYMERASE NUCLEOTIDYLTRANSFERASE POXVIRUS HETERODIMER PROCESSIVITY TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF THE VACCINIA VIRUS POLYADENYL POLYMERASE HETERODIMER: INSIGHTS INTO ATP SELECTIVI PROCESSIVITY. MOL.CELL V. 22 339 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AGS D:482;
D:483;
Valid;
Valid;
none;
none;
submit data
523.247 C10 H16 N5 O12 P3 S c1nc(...
CA D:480;
D:481;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ER9 2.06 Å EC: 2.1.1.57 CRYSTAL STRUCTURE OF THE HETERODIMERIC VACCINIA VIRUS MRNA POLYADENYLATE POLYMERASE COMPLEX WITH UU AND 3'-DEOXY ATP VACCINIA VIRUS WR POLYADENYLATE POLYMERASE TRANSLOCATION SINGLE TRANDED RNA POLYMERASE RNA PROTEIN COMPLEX PROCESSIVITY HETERODIMERNUCLEOTIDYLTRANSFERASE POXVIRUS; METHYLTRANSFERASE MRNA CMRNA PROCESSING S-ADENOSYL-L-METHIONINE TRANSCRIPTION TRANSFERASE TRANSFERASE-RNA COMPLEX
Ref.: POLYMERASE TRANSLOCATION WITH RESPECT TO SINGLE-STR NUCLEIC ACID: LOOPING OR WRAPPING OF PRIMER AROUND POLYMERASE STRUCTURE V. 17 680 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3ER9 - U U n/a n/a
2 2GA9 - AGS C10 H16 N5 O12 P3 S 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 3 families.
1 3ER9 - U U n/a n/a
2 2GA9 - AGS C10 H16 N5 O12 P3 S 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 2 families.
1 3ER9 - U U n/a n/a
2 2GA9 - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: AGS; Similar ligands found: 486
No: Ligand ECFP6 Tc MDL keys Tc
1 AGS 1 1
2 BA3 0.887324 0.92
3 B4P 0.875 0.92
4 AP5 0.875 0.92
5 A2D 0.859155 0.92
6 ATP 0.84 0.945946
7 HEJ 0.84 0.945946
8 5FA 0.828947 0.945946
9 AQP 0.828947 0.945946
10 AN2 0.813333 0.933333
11 ADP 0.8 0.945946
12 AT4 0.789474 0.986486
13 APR 0.782051 0.92
14 AR6 0.782051 0.92
15 M33 0.779221 0.907895
16 AD9 0.772152 0.921053
17 ACP 0.769231 0.921053
18 HQG 0.759036 0.933333
19 SRA 0.756757 0.972973
20 A22 0.75 0.933333
21 50T 0.746835 0.907895
22 AMP 0.743243 0.918919
23 A 0.743243 0.918919
24 ADX 0.734177 0.9
25 CA0 0.734177 0.896104
26 ADQ 0.732558 0.896104
27 ANP 0.731707 0.921053
28 ACQ 0.731707 0.921053
29 25L 0.730337 0.933333
30 6YZ 0.72619 0.921053
31 KG4 0.725 0.896104
32 PRX 0.716049 0.848101
33 9X8 0.715909 0.947368
34 OAD 0.715909 0.896104
35 ATF 0.714286 0.909091
36 45A 0.714286 0.87013
37 ABM 0.714286 0.87013
38 AMP MG 0.710526 0.88
39 JNT 0.704545 0.896104
40 A12 0.696203 0.909091
41 AP2 0.696203 0.909091
42 A1R 0.693182 0.8625
43 A3R 0.693182 0.8625
44 T99 0.690476 0.986486
45 TAT 0.690476 0.986486
46 5AL 0.682353 0.883117
47 8LE 0.682353 0.85
48 25A 0.681818 0.92
49 3OD 0.681319 0.896104
50 ADP MG 0.679012 0.893333
51 ADP BEF 0.679012 0.893333
52 APC 0.674699 0.909091
53 AU1 0.670732 0.921053
54 SRP 0.666667 0.860759
55 APC MG 0.666667 0.87013
56 8LH 0.666667 0.860759
57 KMQ 0.659574 0.884615
58 G3A 0.65625 0.875
59 4AD 0.655556 0.873418
60 QA7 0.651685 0.85
61 8LQ 0.651685 0.860759
62 G5P 0.649485 0.875
63 AFH 0.649485 0.841463
64 00A 0.648352 0.839506
65 ADP PO3 0.647059 0.893333
66 ATP MG 0.647059 0.893333
67 RBY 0.647059 0.884615
68 ADV 0.647059 0.884615
69 BIS 0.645161 0.886076
70 OZV 0.644444 0.92
71 5SV 0.644444 0.807229
72 8QN 0.644444 0.883117
73 OOB 0.644444 0.883117
74 GTA 0.642857 0.843373
75 BEF ADP 0.639535 0.87013
76 PAJ 0.637363 0.841463
77 AMO 0.637363 0.884615
78 VO4 ADP 0.636364 0.896104
79 ITT 0.630952 0.893333
80 DLL 0.630435 0.883117
81 AHX 0.630435 0.851852
82 NB8 0.62766 0.851852
83 V2G 0.625 0.851852
84 UP5 0.623762 0.873418
85 3UK 0.623656 0.871795
86 SON 0.619048 0.884615
87 ANP MG 0.617977 0.883117
88 ALF ADP 0.617977 0.82716
89 OMR 0.617647 0.811765
90 WAQ 0.617021 0.839506
91 LAD 0.617021 0.819277
92 B5V 0.617021 0.860759
93 PR8 0.617021 0.809524
94 DAL AMP 0.615385 0.858974
95 MAP 0.615385 0.897436
96 GAP 0.613636 0.848101
97 LMS 0.6125 0.853659
98 7D4 0.611765 0.858974
99 1ZZ 0.610526 0.8
100 ME8 0.610526 0.821429
101 PTJ 0.610526 0.851852
102 FYA 0.610526 0.858974
103 TXA 0.610526 0.884615
104 DQV 0.61 0.907895
105 PAP 0.609195 0.932432
106 ATR 0.609195 0.918919
107 6V0 0.607843 0.851852
108 NAX 0.607843 0.831325
109 NAI 0.607843 0.8625
110 ADP BMA 0.606383 0.871795
111 A4P 0.605769 0.804598
112 A2R 0.604396 0.933333
113 RAB 0.60274 0.8
114 ADN 0.60274 0.8
115 XYA 0.60274 0.8
116 48N 0.598039 0.851852
117 9SN 0.597938 0.829268
118 139 0.59434 0.831325
119 T5A 0.59434 0.802326
120 TXD 0.592233 0.8625
121 DND 0.592233 0.884615
122 B5Y 0.591837 0.85
123 B5M 0.591837 0.85
124 FA5 0.591837 0.860759
125 9ZD 0.591398 0.8625
126 9ZA 0.591398 0.8625
127 TXE 0.586538 0.8625
128 XAH 0.585859 0.8
129 HFD 0.58427 0.897436
130 JSQ 0.58427 0.897436
131 GA7 0.584158 0.860759
132 AP0 0.580952 0.851852
133 L3W 0.580952 0.884615
134 4UV 0.58 0.85
135 2A5 0.579545 0.871795
136 AOC 0.578313 0.779221
137 COD 0.577982 0.795455
138 A3P 0.576471 0.918919
139 ATP A A A 0.575758 0.881579
140 ATP A 0.575758 0.881579
141 CNA 0.574074 0.884615
142 LAQ 0.572816 0.865854
143 5AS 0.569767 0.804598
144 4UU 0.568627 0.85
145 YLP 0.567308 0.781609
146 4TC 0.566038 0.851852
147 YLB 0.566038 0.781609
148 UPA 0.566038 0.8625
149 5N5 0.565789 0.776316
150 ADJ 0.564815 0.811765
151 7D3 0.564706 0.858974
152 3AM 0.560976 0.88
153 A4D 0.558442 0.8
154 5CD 0.558442 0.763158
155 A2P 0.55814 0.905405
156 NA7 0.556701 0.909091
157 F2R 0.554545 0.823529
158 PPS 0.554348 0.9
159 H1Q 0.550562 0.857143
160 G5A 0.549451 0.804598
161 GSP 0.547368 0.924051
162 4UW 0.54717 0.819277
163 JB6 0.545455 0.910256
164 3AT 0.543478 0.92
165 TYM 0.542056 0.860759
166 MYR AMP 0.54 0.77907
167 80F 0.539823 0.845238
168 AR6 AR6 0.538462 0.87013
169 EP4 0.5375 0.716049
170 YLC 0.537037 0.8
171 7D5 0.536585 0.833333
172 NAD 0.535714 0.883117
173 DTA 0.530864 0.792208
174 M2T 0.530864 0.719512
175 2AM 0.53012 0.893333
176 3DH 0.53012 0.75641
177 AHZ 0.528302 0.821429
178 IOT 0.527273 0.793103
179 DTP 0.526882 0.858974
180 A3D 0.526316 0.871795
181 SSA 0.526316 0.825581
182 MTA 0.52439 0.75641
183 ARG AMP 0.52381 0.790698
184 YLA 0.522523 0.781609
185 BTX 0.522124 0.845238
186 6AD 0.521277 0.911392
187 AMP DBH 0.519231 0.848101
188 TAD 0.518868 0.8875
189 AYB 0.517857 0.772727
190 BT5 0.517544 0.835294
191 A5A 0.515789 0.833333
192 TSB 0.515464 0.845238
193 OVE 0.511628 0.933333
194 6RE 0.511628 0.722892
195 7DT 0.51087 0.932432
196 V3L 0.510638 0.92
197 AVV 0.510204 0.851852
198 7MD 0.509434 0.821429
199 LPA AMP 0.509259 0.843373
200 0WD 0.508772 0.875
201 NAE 0.508475 0.85
202 VMS 0.505155 0.813953
203 54H 0.505155 0.813953
204 NO7 0.505155 0.884615
205 52H 0.505155 0.804598
206 NSS 0.50505 0.825581
207 NAQ 0.504202 0.829268
208 EAD 0.504132 0.831325
209 FB0 0.504 0.769231
210 53H 0.5 0.804598
211 ALF ADP 3PG 0.5 0.797619
212 ZID 0.5 0.871795
213 CUU 0.5 0.92
214 IMO 0.5 0.88
215 J7C 0.5 0.731707
216 ZAS 0.5 0.728395
217 38V 0.5 0.843373
218 8X1 0.5 0.777778
219 AV2 0.5 0.87013
220 AF3 ADP 3PG 0.5 0.797619
221 RGT 0.5 0.909091
222 NJP 0.5 0.897436
223 NVA LMS 0.5 0.777778
224 M24 0.5 0.809524
225 5CA 0.5 0.825581
226 ARU 0.5 0.819277
227 A3N 0.5 0.746835
228 D4F 0.495798 0.843373
229 NPW 0.495575 0.843373
230 NDP 0.495575 0.875
231 NAD TDB 0.495495 0.87013
232 NAD IBO 0.495495 0.87013
233 LEU LMS 0.49505 0.736264
234 DDS 0.494737 0.833333
235 S4M 0.494382 0.655556
236 6MZ 0.494382 0.881579
237 6FA 0.492188 0.802326
238 DZD 0.491379 0.841463
239 NZQ 0.491228 0.864198
240 P5A 0.490196 0.769231
241 LSS 0.49 0.786517
242 DSZ 0.49 0.825581
243 MAO 0.488889 0.724138
244 DSH 0.488636 0.710843
245 P1H 0.488 0.811765
246 N0B 0.487603 0.781609
247 YLY 0.487395 0.772727
248 ODP 0.486957 0.864198
249 8PZ 0.485714 0.825581
250 9K8 0.485437 0.758242
251 FAS 0.484615 0.811765
252 FAD 0.484615 0.811765
253 SFD 0.484615 0.776596
254 FDA 0.484375 0.795455
255 O02 0.484211 0.875
256 DAT 0.483871 0.858974
257 5X8 0.483871 0.746835
258 NAJ PZO 0.483051 0.807229
259 7MC 0.482143 0.802326
260 NWW 0.481481 0.72
261 62F 0.481203 0.821429
262 LQJ 0.481132 0.87013
263 PO4 PO4 A A A A PO4 0.480392 0.855263
264 7DD 0.478261 0.932432
265 TXP 0.478261 0.875
266 GJV 0.477778 0.714286
267 NDE 0.47619 0.884615
268 KAA 0.475728 0.777778
269 GSU 0.475728 0.804598
270 5AD 0.474359 0.706667
271 A3G 0.47191 0.759494
272 K3K 0.471698 0.7625
273 XNP 0.470085 0.831325
274 AMP NAD 0.470085 0.858974
275 4TA 0.470085 0.770115
276 GP3 0.46875 0.875
277 NDC 0.46875 0.829268
278 6C6 0.46875 0.8375
279 7D7 0.468354 0.705128
280 SFG 0.468085 0.7125
281 YSA 0.46729 0.804598
282 NAJ PYZ 0.467213 0.770115
283 FAY 0.466667 0.821429
284 DCA 0.466667 0.786517
285 ETB 0.466667 0.795455
286 128 0.464286 0.741573
287 RFL 0.463235 0.784091
288 PUA 0.46281 0.841463
289 A7D 0.462366 0.759494
290 FNK 0.459259 0.769231
291 0T1 0.459016 0.786517
292 COA 0.459016 0.806818
293 7C5 0.458716 0.777778
294 A5D 0.458333 0.792208
295 SA8 0.458333 0.674419
296 MHZ 0.457447 0.666667
297 71V 0.456522 0.910256
298 8Q2 0.45614 0.797753
299 NEC 0.455556 0.708861
300 GGZ 0.455446 0.851852
301 B1U 0.453704 0.76087
302 SAH 0.453608 0.728395
303 SAI 0.453608 0.698795
304 Y3J 0.451219 0.688312
305 GEK 0.45098 0.722892
306 AS 0.450549 0.884615
307 4YB 0.45045 0.786517
308 SMM 0.45 0.674157
309 GTP 0.45 0.873418
310 V47 0.45 0.74359
311 K3E 0.449541 0.753086
312 6IA 0.44898 0.797619
313 SAM 0.44898 0.678161
314 AMX 0.448 0.795455
315 COS 0.448 0.808989
316 CAO 0.448 0.8
317 30N 0.448 0.776596
318 TAP 0.448 0.935065
319 J4G 0.447619 0.873418
320 SCO 0.444444 0.786517
321 AAT 0.444444 0.714286
322 CMX 0.444444 0.786517
323 EEM 0.444444 0.659091
324 P5F 0.443662 0.786517
325 KOY 0.442478 0.7625
326 PGS 0.442105 0.910256
327 FCX 0.440945 0.76087
328 ACO 0.440945 0.8
329 FAM 0.440945 0.769231
330 2SA 0.44 0.884615
331 HDV 0.44 0.848101
332 NAP 0.44 0.896104
333 9JJ 0.439716 0.821429
334 APU 0.439655 0.85
335 D5M 0.43956 0.833333
336 DA 0.43956 0.833333
337 HAX 0.4375 0.769231
338 QXP 0.436893 0.811765
339 Z5A 0.436508 0.744444
340 DG1 0.436508 0.875
341 1DG 0.436508 0.875
342 V1N 0.436364 0.87013
343 S7M 0.435644 0.678161
344 2MC 0.435115 0.774194
345 649 0.434783 0.769231
346 WSA 0.434783 0.813953
347 AAM 0.434783 0.918919
348 CZF 0.434343 0.883117
349 3KK 0.434109 0.808989
350 FYN 0.434109 0.806818
351 NMN AMP PO4 0.433333 0.82716
352 7L1 0.433071 0.8
353 NA0 0.433071 0.884615
354 C2R 0.431818 0.857143
355 AMZ 0.431818 0.868421
356 A3S 0.431579 0.769231
357 SOP 0.430769 0.788889
358 CA6 0.430769 0.752577
359 YZS 0.430769 0.770833
360 MCD 0.430769 0.769231
361 KGP 0.430769 0.770833
362 OXK 0.430769 0.808989
363 COK 0.430769 0.808989
364 QBQ 0.43 0.860759
365 GNH 0.43 0.8625
366 62X 0.428571 0.637363
367 101 0.428571 0.833333
368 N6P 0.428571 0.866667
369 NVA 2AD 0.428571 0.722892
370 F2N 0.427586 0.777778
371 CO6 0.427481 0.808989
372 CMC 0.427481 0.788889
373 NMX 0.427481 0.729167
374 1VU 0.427481 0.8
375 GKE 0.427273 0.841463
376 GDC 0.427273 0.841463
377 K2W 0.427273 0.705882
378 GDD 0.427273 0.841463
379 NWQ 0.426966 0.701299
380 SCA 0.425373 0.808989
381 9BG 0.425 0.851852
382 FA9 0.424658 0.823529
383 A6D 0.424528 0.729412
384 QXG 0.424528 0.802326
385 K15 0.424528 0.651685
386 CAJ 0.424242 0.769231
387 SCD 0.424242 0.786517
388 N5O 0.423913 0.725
389 AIR 0.423529 0.853333
390 6K6 0.423077 0.881579
391 A3T 0.42268 0.779221
392 NIA 0.422222 0.783133
393 KGA 0.422222 0.714286
394 K38 0.422018 0.740741
395 NHD 0.421488 0.858974
396 KGJ 0.421053 0.721649
397 3HC 0.421053 0.818182
398 IVC 0.421053 0.818182
399 MLC 0.421053 0.808989
400 BCO 0.421053 0.808989
401 1HE 0.421053 0.791209
402 A1S 0.421053 0.788889
403 12D 0.421053 0.75
404 R2V 0.420561 0.811765
405 1CZ 0.42029 0.820225
406 GDP 0.42 0.873418
407 0UM 0.419048 0.666667
408 FAJ 0.418919 0.793103
409 CAA 0.41791 0.818182
410 COO 0.41791 0.808989
411 MCA 0.41791 0.8
412 LCV 0.41791 0.762887
413 YE1 0.41791 0.777778
414 SO5 0.41791 0.762887
415 GCP 0.417476 0.851852
416 G1R 0.417476 0.8625
417 OZP 0.417391 0.694118
418 NAD CJ3 0.417266 0.837209
419 SXZ 0.416667 0.697674
420 O05 0.416667 0.804598
421 K2H 0.415094 0.719512
422 N5A 0.414894 0.7
423 YXS 0.414815 0.770833
424 MC4 0.414815 0.765957
425 YXR 0.414815 0.770833
426 2CP 0.414815 0.78022
427 K3H 0.414414 0.714286
428 ZDA 0.414141 0.820513
429 KY2 0.413462 0.697674
430 NAD BBN 0.413043 0.802326
431 KB1 0.412844 0.666667
432 COW 0.411765 0.8
433 KFV 0.411765 0.742268
434 IRC 0.411765 0.818182
435 1GZ 0.411765 0.8
436 HGG 0.411765 0.808989
437 MGP 0.411765 0.841463
438 BYC 0.411765 0.808989
439 3AD 0.411765 0.763158
440 3CP 0.411765 0.788889
441 2KQ 0.411765 0.791209
442 CA8 0.411765 0.770833
443 COF 0.411765 0.771739
444 N01 0.41129 0.858974
445 PLP AAD 0.41129 0.73913
446 S8M 0.409524 0.743902
447 COA FLC 0.409449 0.775281
448 FAQ 0.408759 0.808989
449 BCA 0.408759 0.8
450 4CA 0.408759 0.78022
451 7RP 0.408602 0.878378
452 2VA 0.408163 0.759494
453 6G0 0.407767 0.841463
454 CO7 0.407407 0.808989
455 K2K 0.407407 0.702381
456 26A 0.406977 0.725
457 Q34 0.40678 0.644444
458 QQX 0.406593 0.857143
459 GRA 0.405797 0.808989
460 HXC 0.405797 0.791209
461 KYB 0.40566 0.697674
462 KL2 0.404494 0.794872
463 7RA 0.404255 0.906667
464 FAI 0.404255 0.868421
465 GPG 0.40367 0.864198
466 K2R 0.40367 0.835443
467 TGC 0.402878 0.8
468 SP1 0.402174 0.894737
469 QQY 0.402174 0.844156
470 RP1 0.402174 0.894737
471 ACK 0.402174 0.815789
472 DZ4 0.401961 0.8375
473 KYE 0.401786 0.681818
474 APC G U 0.401575 0.795181
475 8BR 0.4 0.860759
476 KY5 0.4 0.690476
477 9GM 0.4 0.851852
478 GNP 0.4 0.851852
479 SLU 0.4 0.816092
480 KXW 0.4 0.674419
481 S0N 0.4 0.769231
482 CO8 0.4 0.791209
483 CIC 0.4 0.788889
484 2NE 0.4 0.791209
485 TM1 0.4 0.738636
486 EO7 0.4 0.813953
Similar Ligands (3D)
Ligand no: 1; Ligand: AGS; Similar ligands found: 27
No: Ligand Similarity coefficient
1 ADP ALF 0.9782
2 ADP AF3 0.9674
3 GDP AF3 0.9569
4 ALF GDP 0.9557
5 GDP ALF 0.9520
6 GDP BEF 0.9444
7 DBG 0.9424
8 BEF GDP 0.9401
9 DGT 0.9355
10 UTP 0.9231
11 CTP 0.9211
12 2KH 0.9090
13 DCP 0.9032
14 GH3 0.9015
15 TTP 0.8934
16 GDP MG 0.8916
17 Y9Z 0.8809
18 ALF 5GP 0.8802
19 NYZ 0.8703
20 IDP 0.8674
21 NX8 0.8652
22 D3T 0.8642
23 DGI 0.8617
24 8DG 0.8610
25 GP2 0.8595
26 DUP 0.8579
27 M7G 0.8576
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ER9; Ligand: 3AT; 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: 3er9.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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