Receptor
PDB id Resolution Class Description Source Keywords
3BHO 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE 25KDA SUBUNIT OF HUMAN CLEAVAGE FAC WITH AP4A HOMO SAPIENS CPSF5 RNA PROCESSING CLEAVAGE FACTOR DIADENOSINE TETRAPHOMRNA PROCESSING NUCLEUS PHOSPHOPROTEIN RNA-BINDING NUCLPROTEIN
Ref.: CRYSTAL STRUCTURE OF THE 25 KDA SUBUNIT OF HUMAN CL FACTOR IM. NUCLEIC ACIDS RES. V. 36 3474 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B4P A:800;
Valid;
none;
Kd = 2.44 uM
836.387 C20 H28 N10 O19 P4 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BHO 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE 25KDA SUBUNIT OF HUMAN CLEAVAGE FAC WITH AP4A HOMO SAPIENS CPSF5 RNA PROCESSING CLEAVAGE FACTOR DIADENOSINE TETRAPHOMRNA PROCESSING NUCLEUS PHOSPHOPROTEIN RNA-BINDING NUCLPROTEIN
Ref.: CRYSTAL STRUCTURE OF THE 25 KDA SUBUNIT OF HUMAN CL FACTOR IM. NUCLEIC ACIDS RES. V. 36 3474 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 3BHO Kd = 2.44 uM B4P C20 H28 N10 O19 P4 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 1331 families.
1 3BHO Kd = 2.44 uM B4P C20 H28 N10 O19 P4 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 1144 families.
1 3BHO Kd = 2.44 uM B4P C20 H28 N10 O19 P4 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: B4P; Similar ligands found: 491
No: Ligand ECFP6 Tc MDL keys Tc
1 B4P 1 1
2 AP5 1 1
3 BA3 0.984615 1
4 AQP 0.942029 0.971831
5 5FA 0.942029 0.971831
6 ATP 0.927536 0.971831
7 HEJ 0.927536 0.971831
8 A2D 0.924242 1
9 ADP 0.884058 0.971831
10 AGS 0.875 0.92
11 AT4 0.84507 0.932432
12 AN2 0.84507 0.958333
13 APR 0.835616 0.971831
14 AR6 0.835616 0.971831
15 M33 0.833333 0.958333
16 AD9 0.824324 0.945205
17 ACP 0.821918 0.945205
18 ACQ 0.802632 0.945205
19 ANP 0.802632 0.945205
20 A 0.797101 0.943662
21 AMP 0.797101 0.943662
22 6YZ 0.794872 0.945205
23 ADX 0.783784 0.873418
24 CA0 0.783784 0.945205
25 KG4 0.773333 0.945205
26 50T 0.773333 0.931507
27 45A 0.763889 0.917808
28 ABM 0.763889 0.917808
29 PRX 0.763158 0.893333
30 HQG 0.7625 0.958333
31 AMP MG 0.760563 0.929577
32 ATF 0.759494 0.932432
33 T99 0.75641 0.932432
34 TAT 0.75641 0.932432
35 A22 0.753086 0.985915
36 25L 0.752941 0.985915
37 AP2 0.743243 0.932432
38 A12 0.743243 0.932432
39 APC 0.74026 0.932432
40 SRA 0.736111 0.893333
41 A3R 0.73494 0.907895
42 ADQ 0.73494 0.972222
43 A1R 0.73494 0.907895
44 JNT 0.72619 0.945205
45 8LE 0.725 0.894737
46 5AL 0.725 0.931507
47 ADP BEF 0.723684 0.943662
48 ADP MG 0.723684 0.943662
49 G5P 0.722222 0.921053
50 9X8 0.717647 0.92
51 OAD 0.717647 0.945205
52 AU1 0.714286 0.945205
53 G3A 0.711111 0.921053
54 APC MG 0.708861 0.917808
55 SRP 0.707317 0.906667
56 8LH 0.707317 0.906667
57 8QN 0.702381 0.931507
58 3OD 0.701149 0.945205
59 GTA 0.695652 0.886076
60 4AD 0.694118 0.92
61 UP5 0.691489 0.945946
62 QA7 0.690476 0.894737
63 8LQ 0.690476 0.906667
64 ATP MG 0.6875 0.943662
65 RBY 0.6875 0.932432
66 ADP PO3 0.6875 0.943662
67 ADV 0.6875 0.932432
68 00A 0.686047 0.907895
69 OOB 0.682353 0.958333
70 25A 0.682353 0.971831
71 5SV 0.682353 0.848101
72 OZV 0.682353 0.971831
73 BIS 0.681818 0.907895
74 BEF ADP 0.679012 0.917808
75 KMQ 0.677778 0.932432
76 VO4 ADP 0.674699 0.918919
77 PAJ 0.674419 0.884615
78 AMO 0.674419 0.932432
79 7D4 0.670886 0.88
80 ITT 0.670886 0.916667
81 MAP 0.670588 0.92
82 A4P 0.670103 0.843373
83 DLL 0.666667 0.958333
84 AHX 0.666667 0.896104
85 V2G 0.662651 0.871795
86 3UK 0.659091 0.945205
87 SON 0.658228 0.906667
88 T5A 0.656566 0.864198
89 ANP MG 0.654762 0.931507
90 ALF ADP 0.654762 0.87013
91 LMS 0.653333 0.82716
92 PR8 0.651685 0.85
93 B5V 0.651685 0.932432
94 WAQ 0.651685 0.883117
95 LAD 0.651685 0.860759
96 GAP 0.650602 0.893333
97 AFH 0.648936 0.909091
98 TXA 0.644444 0.932432
99 NB8 0.644444 0.896104
100 1ZZ 0.644444 0.839506
101 FYA 0.644444 0.931507
102 PTJ 0.644444 0.871795
103 ME8 0.644444 0.839506
104 DQV 0.642105 0.985915
105 JSQ 0.638554 0.92
106 HFD 0.638554 0.92
107 2A5 0.634146 0.893333
108 DAL AMP 0.632184 0.905405
109 9SN 0.630435 0.896104
110 48N 0.628866 0.896104
111 PAP 0.626506 0.957747
112 ATR 0.626506 0.943662
113 9ZA 0.625 0.883117
114 9ZD 0.625 0.883117
115 B5M 0.623656 0.92
116 B5Y 0.623656 0.92
117 FA5 0.623656 0.932432
118 RAB 0.623188 0.84507
119 XYA 0.623188 0.84507
120 ADN 0.623188 0.84507
121 6V0 0.622449 0.921053
122 DND 0.622449 0.958904
123 NAI 0.622449 0.933333
124 NAX 0.622449 0.897436
125 TXD 0.622449 0.933333
126 7D3 0.620253 0.88
127 XAH 0.617021 0.839506
128 TXE 0.616162 0.933333
129 OMR 0.616162 0.851852
130 AOC 0.615385 0.821918
131 4UV 0.610526 0.92
132 AP0 0.61 0.921053
133 L3W 0.61 0.932432
134 5N5 0.605634 0.819444
135 5AS 0.604938 0.77907
136 ADP BMA 0.604396 0.945205
137 A2R 0.602273 0.958333
138 CNA 0.601942 0.958904
139 4UU 0.597938 0.92
140 GA7 0.597938 0.932432
141 5CD 0.597222 0.805556
142 A4D 0.597222 0.819444
143 4TC 0.594059 0.921053
144 3AT 0.593023 0.944444
145 139 0.592233 0.897436
146 ADJ 0.592233 0.875
147 LAQ 0.585859 0.839506
148 F2R 0.580952 0.841463
149 YLP 0.58 0.819277
150 COD 0.575472 0.811765
151 DTP 0.574713 0.88
152 JB6 0.574468 0.907895
153 4UW 0.574257 0.884615
154 EP4 0.573333 0.753247
155 A3P 0.573171 0.943662
156 ATP A A A 0.572917 0.957747
157 ATP A 0.572917 0.957747
158 7D5 0.571429 0.853333
159 TYM 0.568627 0.932432
160 MYR AMP 0.568421 0.817073
161 6AD 0.568182 0.884615
162 DTA 0.565789 0.810811
163 M2T 0.565789 0.734177
164 80F 0.564815 0.864198
165 H1Q 0.564706 0.90411
166 3DH 0.564103 0.773333
167 G5A 0.563218 0.77907
168 UPA 0.563107 0.933333
169 YLC 0.563107 0.839506
170 YLB 0.563107 0.819277
171 NAD 0.560748 0.958333
172 TSB 0.56044 0.819277
173 MTA 0.558442 0.773333
174 3AM 0.556962 0.902778
175 SSA 0.555556 0.8
176 AHZ 0.554455 0.817073
177 A2P 0.554217 0.929577
178 NA7 0.553191 0.932432
179 IOT 0.552381 0.809524
180 PPS 0.550562 0.85
181 A3D 0.550459 0.945205
182 7MD 0.55 0.8625
183 ARG AMP 0.55 0.807229
184 AR6 AR6 0.55 0.944444
185 NO7 0.549451 0.906667
186 54H 0.549451 0.788235
187 VMS 0.549451 0.788235
188 YLA 0.54717 0.819277
189 CUU 0.546512 0.944444
190 AMP DBH 0.545455 0.918919
191 TAD 0.544554 0.884615
192 AV2 0.544444 0.891892
193 A5A 0.544444 0.807229
194 6RE 0.54321 0.7375
195 AYB 0.542056 0.809524
196 7DT 0.54023 0.957747
197 DDS 0.539326 0.853333
198 AVV 0.537634 0.896104
199 52H 0.532609 0.77907
200 BTX 0.53211 0.819277
201 NSS 0.531915 0.8
202 NAE 0.530973 0.92
203 ZAS 0.530864 0.766234
204 A3N 0.53012 0.786667
205 IMO 0.53012 0.902778
206 J7C 0.53012 0.746835
207 DAT 0.528736 0.88
208 BT5 0.527273 0.809524
209 53H 0.526882 0.77907
210 5CA 0.526882 0.8
211 8X1 0.526882 0.752809
212 NVA LMS 0.526316 0.752809
213 NAQ 0.526316 0.896104
214 ARU 0.526316 0.8375
215 EAD 0.525862 0.897436
216 9K8 0.525773 0.733333
217 RGT 0.525253 0.932432
218 2AM 0.525 0.916667
219 AF3 ADP 3PG 0.52381 0.8375
220 ALF ADP 3PG 0.52381 0.8375
221 6MZ 0.52381 0.90411
222 S4M 0.52381 0.666667
223 V3L 0.522222 0.944444
224 ZID 0.521739 0.945205
225 LEU LMS 0.520833 0.730337
226 LPA AMP 0.519231 0.817073
227 NAD IBO 0.518868 0.944444
228 7MC 0.518868 0.841463
229 NAD TDB 0.518868 0.944444
230 DSH 0.518072 0.725
231 MAO 0.517647 0.759036
232 D4F 0.517544 0.8625
233 LSS 0.515789 0.761364
234 DSZ 0.515789 0.8
235 P5A 0.515464 0.744444
236 DZD 0.513514 0.909091
237 NWW 0.513158 0.760563
238 FB0 0.512397 0.784091
239 5X8 0.511364 0.763158
240 O02 0.511111 0.896104
241 GP3 0.511111 0.921053
242 YLY 0.508772 0.809524
243 M24 0.508772 0.873418
244 38V 0.508621 0.886076
245 N0B 0.508621 0.841463
246 P1H 0.508333 0.875
247 5AD 0.506849 0.746479
248 OVE 0.506024 0.88
249 GJV 0.505882 0.728395
250 7DD 0.505747 0.957747
251 NAJ PZO 0.504425 0.871795
252 NEC 0.5 0.746667
253 GSU 0.5 0.77907
254 128 0.5 0.776471
255 KAA 0.5 0.752809
256 NDE 0.495868 0.932432
257 NJP 0.495495 0.945946
258 6C6 0.494505 0.857143
259 SFG 0.494382 0.75
260 FDA 0.491935 0.833333
261 AMP NAD 0.491071 0.931507
262 4TA 0.491071 0.829268
263 0WD 0.491071 0.921053
264 YSA 0.490196 0.8
265 GTP 0.489362 0.894737
266 A7D 0.488636 0.776316
267 6FA 0.488 0.864198
268 NDC 0.487805 0.896104
269 NAJ PYZ 0.487179 0.829268
270 SA8 0.483516 0.707317
271 A5D 0.483516 0.810811
272 MHZ 0.483146 0.697674
273 71V 0.482759 0.883117
274 A3G 0.482353 0.8
275 ODP 0.482143 0.909091
276 Y3J 0.480519 0.726027
277 K3K 0.480392 0.826667
278 8PZ 0.480392 0.821429
279 FAS 0.480315 0.875
280 FAD 0.480315 0.875
281 SFD 0.480315 0.752688
282 7D7 0.48 0.743243
283 GGZ 0.479167 0.825
284 HDV 0.478723 0.868421
285 SAH 0.478261 0.74359
286 SAI 0.478261 0.734177
287 NDP 0.477477 0.921053
288 NPW 0.477477 0.886076
289 LQJ 0.475728 0.944444
290 B1U 0.475728 0.755556
291 PO4 PO4 A A A A PO4 0.474747 0.929577
292 SMM 0.473684 0.686047
293 TXP 0.473214 0.921053
294 NZQ 0.473214 0.909091
295 6IA 0.473118 0.814815
296 SAM 0.473118 0.690476
297 CZF 0.473118 0.905405
298 K3E 0.471154 0.815789
299 J4G 0.47 0.894737
300 NWQ 0.46988 0.739726
301 AAT 0.468085 0.707317
302 QBQ 0.468085 0.881579
303 EEM 0.468085 0.690476
304 PGS 0.466667 0.858974
305 7C5 0.466667 0.818182
306 62F 0.465649 0.886076
307 FNK 0.465649 0.804598
308 D5M 0.465116 0.853333
309 N5O 0.465116 0.763158
310 DA 0.465116 0.853333
311 N6P 0.464646 0.915493
312 GSP 0.463918 0.85
313 2SA 0.463158 0.906667
314 KOY 0.462963 0.826667
315 FAY 0.462121 0.886076
316 A3T 0.461538 0.821918
317 AAM 0.45977 0.943662
318 QXP 0.459184 0.785714
319 GEK 0.459184 0.7375
320 RFL 0.458647 0.843373
321 S7M 0.458333 0.690476
322 V47 0.458333 0.808219
323 6G0 0.458333 0.860759
324 4YB 0.457944 0.781609
325 AMZ 0.457831 0.890411
326 C2R 0.457831 0.878378
327 GDP 0.457447 0.894737
328 A3S 0.455556 0.810811
329 WSA 0.454545 0.809524
330 N5A 0.454545 0.736842
331 Z5A 0.454545 0.8
332 12D 0.453704 0.785714
333 XNP 0.452174 0.873418
334 8Q2 0.45045 0.793103
335 AIR 0.45 0.875
336 62X 0.45 0.666667
337 ETB 0.449153 0.811765
338 DCA 0.449153 0.802326
339 MGP 0.447917 0.860759
340 NIA 0.447059 0.8
341 QXG 0.445545 0.776471
342 K15 0.445545 0.682353
343 A6D 0.445545 0.743902
344 PUA 0.445378 0.884615
345 9JJ 0.445255 0.886076
346 6K6 0.444444 0.90411
347 V1N 0.443396 0.944444
348 COA 0.441667 0.802326
349 0T1 0.441667 0.802326
350 649 0.441441 0.764045
351 R2V 0.441176 0.785714
352 0UM 0.44 0.698795
353 P5F 0.438849 0.823529
354 GCP 0.438776 0.871795
355 G1R 0.438776 0.883117
356 3AD 0.4375 0.805556
357 DZ4 0.4375 0.857143
358 GNH 0.4375 0.883117
359 O05 0.436893 0.843373
360 K2R 0.436893 0.88
361 101 0.436782 0.853333
362 NVA 2AD 0.43617 0.759494
363 K2H 0.435644 0.779221
364 NAP 0.434426 0.945205
365 GNP 0.434343 0.871795
366 9GM 0.434343 0.871795
367 KY2 0.434343 0.710843
368 K2W 0.433962 0.7625
369 APU 0.433628 0.894737
370 KB1 0.432692 0.719512
371 F2N 0.432624 0.813953
372 7RP 0.431818 0.901408
373 CAO 0.430894 0.775281
374 30N 0.430894 0.734043
375 1DG 0.430894 0.921053
376 DG1 0.430894 0.921053
377 TAP 0.430894 0.907895
378 COS 0.430894 0.784091
379 AMX 0.430894 0.811765
380 2VA 0.430108 0.8
381 S8M 0.43 0.759494
382 GTG 0.429907 0.886076
383 FA9 0.429577 0.864198
384 K38 0.428571 0.802632
385 MGO 0.428571 0.8375
386 KL2 0.428571 0.813333
387 CMX 0.427419 0.802326
388 SCO 0.427419 0.802326
389 NA0 0.427419 0.932432
390 NHD 0.42735 0.931507
391 K2K 0.427184 0.759494
392 NX8 0.427083 0.7375
393 7RA 0.426966 0.930556
394 AS 0.426966 0.810127
395 KYB 0.425743 0.710843
396 ACK 0.425287 0.861111
397 QQY 0.425287 0.815789
398 Q34 0.424779 0.694118
399 FCX 0.424 0.775281
400 ACO 0.424 0.775281
401 FAM 0.424 0.784091
402 FAJ 0.423611 0.853659
403 OZP 0.423423 0.75
404 CC5 0.423077 0.816901
405 SXZ 0.423077 0.710843
406 8BR 0.422222 0.881579
407 EO7 0.422222 0.788235
408 IDP 0.421053 0.893333
409 ZDA 0.421053 0.84
410 HAX 0.420635 0.784091
411 GDD 0.420561 0.884615
412 K3H 0.420561 0.772152
413 GDC 0.420561 0.884615
414 GKE 0.420561 0.884615
415 KYE 0.420561 0.694118
416 J7V 0.419355 0.833333
417 KY5 0.419048 0.746835
418 TM1 0.419048 0.77381
419 9BG 0.418803 0.896104
420 2MC 0.418605 0.75
421 KXW 0.418182 0.728395
422 NAD BBN 0.41791 0.864198
423 CMP 0.417582 0.928571
424 2BA 0.417582 0.942857
425 3KK 0.417323 0.784091
426 FYN 0.417323 0.802326
427 PLP AAD 0.416667 0.752809
428 SO8 0.416667 0.789474
429 SLU 0.416667 0.790698
430 7L1 0.416 0.775281
431 NMN AMP PO4 0.415254 0.894737
432 Q2P 0.415254 0.694118
433 26A 0.414634 0.763158
434 HF7 0.414141 0.868421
435 KGP 0.414062 0.71134
436 OXK 0.414062 0.784091
437 MCD 0.414062 0.784091
438 SOP 0.414062 0.784091
439 YZS 0.414062 0.71134
440 CA6 0.414062 0.71134
441 COK 0.414062 0.784091
442 QQX 0.413793 0.805195
443 KY8 0.413462 0.75
444 G2R 0.413462 0.860759
445 NAD CJ3 0.411765 0.833333
446 PRT 0.411215 0.905405
447 FAI 0.411111 0.890411
448 RMB 0.411111 0.847222
449 1VU 0.410853 0.775281
450 CMC 0.410853 0.784091
451 CO6 0.410853 0.784091
452 NMX 0.410853 0.741935
453 NWZ 0.410526 0.725
454 RP1 0.409091 0.866667
455 SP1 0.409091 0.866667
456 SCA 0.409091 0.784091
457 1RB 0.409091 0.859155
458 ANZ 0.409091 0.8
459 NFD 0.408333 0.907895
460 CAJ 0.407692 0.784091
461 SCD 0.407692 0.802326
462 KGA 0.406015 0.726316
463 D3Y 0.405941 0.813333
464 KH3 0.405405 0.674419
465 N01 0.404959 0.931507
466 IVC 0.40458 0.793103
467 1HE 0.40458 0.766667
468 A1S 0.40458 0.784091
469 MLC 0.40458 0.784091
470 BCO 0.40458 0.784091
471 KGJ 0.40458 0.734043
472 3HC 0.40458 0.793103
473 5GP 0.404255 0.881579
474 G 0.404255 0.881579
475 R7I 0.40404 0.893333
476 R5I 0.40404 0.893333
477 G2Q 0.403846 0.860759
478 3D1 0.402439 0.773333
479 3L1 0.402439 0.773333
480 VRT 0.402062 0.769231
481 HZ2 0.401786 0.753086
482 YE1 0.401515 0.813953
483 LCV 0.401515 0.704082
484 CAA 0.401515 0.793103
485 MCA 0.401515 0.775281
486 SO5 0.401515 0.704082
487 COO 0.401515 0.784091
488 Q2M 0.4 0.690476
489 3NZ 0.4 0.805195
490 GMV 0.4 0.871795
491 CNV FAD 0.4 0.793103
Similar Ligands (3D)
Ligand no: 1; Ligand: B4P; 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 : 3BHO; Ligand: B4P; 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: 3bho.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3BHO; Ligand: B4P; 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: 3bho.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
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