Receptor
PDB id Resolution Class Description Source Keywords
6DJI 1.75 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ522 HOMO SAPIENS FRAGMENT-BASED DRUG DESIGN HYDROLASE-HYDROLASE INHIBITOR CO
Ref.: IDENTIFICATION OF A LIGAND BINDING HOT SPOT AND STR MOTIFS REPLICATING ASPECTS OF TYROSYL-DNA PHOSPHODI I (TDP1) PHOSPHORYL RECOGNITION BY CRYSTALLOGRAPHIC COCKTAIL SCREENING. NUCLEIC ACIDS RES. V. 47 10134 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:702;
A:704;
A:702;
A:703;
B:703;
A:705;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GOG A:701;
B:701;
Valid;
Valid;
none;
none;
ic50 = 3.1 mM
182.13 C8 H6 O5 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DJJ 1.74 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ532 HOMO SAPIENS FRAGMENT-BASED DRUG DESIGN HYDROLASE
Ref.: IDENTIFICATION OF A LIGAND BINDING HOT SPOT AND STR MOTIFS REPLICATING ASPECTS OF TYROSYL-DNA PHOSPHODI I (TDP1) PHOSPHORYL RECOGNITION BY CRYSTALLOGRAPHIC COCKTAIL SCREENING. NUCLEIC ACIDS RES. V. 47 10134 2019
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GOG; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 GOG 1 1
2 GRE 0.62069 0.913043
3 3GQ 0.566667 0.727273
4 DBH 0.5 0.875
5 SAL 0.484848 0.909091
6 PHT 0.419355 0.727273
Similar Ligands (3D)
Ligand no: 1; Ligand: GOG; Similar ligands found: 626
No: Ligand Similarity coefficient
1 NTM 0.9768
2 KLW 0.9732
3 EJZ 0.9671
4 LSA 0.9602
5 PFB 0.9581
6 GCB 0.9521
7 JUG 0.9507
8 ISE 0.9486
9 G1O 0.9464
10 EVA 0.9451
11 G5V 0.9447
12 UEG 0.9446
13 G3F 0.9445
14 YSO 0.9439
15 3WA 0.9431
16 5WY 0.9426
17 AKH 0.9417
18 PXL 0.9416
19 AEZ 0.9413
20 Q6T 0.9404
21 BGC 0.9396
22 8S0 0.9391
23 QAT 0.9390
24 JBQ 0.9383
25 TTY 0.9380
26 GCS 0.9372
27 NTZ 0.9359
28 HTP 0.9358
29 GIM 0.9353
30 GLC 0.9348
31 32X 0.9347
32 25W 0.9344
33 GCU 0.9343
34 12B 0.9338
35 5WX 0.9333
36 HXX 0.9333
37 GJS 0.9331
38 2ZQ 0.9330
39 GM7 0.9330
40 LGC 0.9329
41 DHQ 0.9327
42 HNQ 0.9324
43 NDM 0.9324
44 G6D 0.9313
45 8XQ 0.9297
46 BNT 0.9296
47 MVL 0.9296
48 IPZ 0.9295
49 GZ8 0.9290
50 YQA 0.9290
51 NOJ 0.9284
52 680 0.9280
53 HLZ 0.9277
54 15L 0.9276
55 3HA 0.9272
56 INS 0.9272
57 IJZ 0.9271
58 FBT 0.9270
59 6F0 0.9266
60 PYQ 0.9266
61 KFH 0.9259
62 TEP 0.9258
63 42C 0.9255
64 PX7 0.9254
65 QAS 0.9253
66 Q7A 0.9253
67 DBJ 0.9250
68 39A 0.9246
69 3M0 0.9243
70 AIN 0.9240
71 JBK 0.9238
72 BDP 0.9236
73 7ZE 0.9234
74 9MG 0.9233
75 6M1 0.9231
76 PE0 0.9231
77 FDB 0.9224
78 7VJ 0.9224
79 ZVO 0.9224
80 XAN 0.9221
81 AZ8 0.9220
82 2ZV 0.9219
83 L7T 0.9218
84 FBG 0.9217
85 AZA 0.9213
86 GUN 0.9211
87 06B 0.9211
88 D3M 0.9211
89 8GK 0.9211
90 SXS 0.9210
91 B57 0.9206
92 3FH 0.9205
93 FOT 0.9203
94 2MN 0.9200
95 GAL 0.9199
96 HFB 0.9198
97 9DG 0.9198
98 M1H 0.9197
99 SHG 0.9197
100 DFB 0.9195
101 JKZ 0.9193
102 IGA 0.9188
103 141 0.9188
104 GIO 0.9188
105 1XN 0.9187
106 OA3 0.9186
107 5NE 0.9186
108 MHK 0.9186
109 3F0 0.9182
110 EXO 0.9182
111 PXM 0.9181
112 UAN 0.9178
113 GTZ 0.9178
114 UNC 0.9177
115 XXR 0.9170
116 5RG 0.9167
117 4HC 0.9165
118 3MG 0.9164
119 KBG 0.9159
120 DPZ 0.9158
121 GOX 0.9158
122 HJP 0.9155
123 495 0.9154
124 KGK 0.9154
125 K5W 0.9152
126 SJ5 0.9149
127 7NI 0.9145
128 BE2 0.9142
129 F5B 0.9142
130 EQT 0.9139
131 B60 0.9134
132 J9W 0.9133
133 HQY 0.9132
134 1NP 0.9131
135 FE DB1 0.9130
136 GT0 0.9130
137 FUC 0.9130
138 N5J 0.9128
139 MEW 0.9127
140 5Q0 0.9127
141 SRO 0.9127
142 1LM 0.9126
143 CFP 0.9125
144 B53 0.9125
145 AQO 0.9123
146 329 0.9122
147 24W 0.9121
148 CFF 0.9121
149 DQN 0.9119
150 Q24 0.9119
151 ENL 0.9118
152 O2A 0.9117
153 A2F 0.9116
154 HZQ 0.9115
155 3C1 0.9112
156 NQ 0.9110
157 KJY 0.9110
158 37T 0.9108
159 9KT 0.9107
160 60Q 0.9106
161 M0Q 0.9103
162 BBF 0.9097
163 GTQ 0.9097
164 1LQ 0.9096
165 HHA 0.9096
166 6M4 0.9093
167 5SG 0.9092
168 VK3 0.9091
169 ES1 0.9089
170 MT0 0.9088
171 5NS 0.9087
172 UQ 0.9086
173 IFM 0.9084
174 5M0 0.9084
175 0W8 0.9083
176 XYP 0.9080
177 M1Q 0.9079
178 4YS 0.9079
179 AZF 0.9079
180 JBE 0.9079
181 E7Z 0.9077
182 PCI 0.9076
183 GYE 0.9076
184 3RK 0.9075
185 1SQ 0.9075
186 MBG 0.9075
187 GCV 0.9074
188 AJ2 0.9070
189 4AA 0.9070
190 6KX 0.9069
191 JPZ 0.9069
192 MAQ 0.9067
193 M0W 0.9066
194 ES6 0.9065
195 5IQ 0.9064
196 ADK 0.9064
197 QPR 0.9064
198 7VS 0.9063
199 ZZ8 0.9061
200 290 0.9061
201 HH8 0.9061
202 MWP 0.9060
203 M5K 0.9060
204 23A 0.9059
205 3C2 0.9058
206 ADZ 0.9057
207 GTR 0.9057
208 RXA 0.9056
209 I3A 0.9055
210 BCF 0.9052
211 6CS 0.9051
212 SVN 0.9049
213 DX4 0.9047
214 PQ0 0.9047
215 FUL 0.9047
216 G2F 0.9046
217 3IT 0.9044
218 9TZ 0.9043
219 AZ9 0.9043
220 JBH 0.9041
221 PRF 0.9039
222 JTH 0.9037
223 MT8 0.9037
224 DHK 0.9037
225 3U4 0.9036
226 6AP 0.9036
227 4ME 0.9034
228 2EC 0.9034
229 7B3 0.9033
230 3SK 0.9032
231 9PY 0.9030
232 5WU 0.9030
233 IBF 0.9028
234 IP0 0.9028
235 R8V 0.9025
236 1XM 0.9025
237 54G 0.9024
238 OXZ 0.9024
239 149 0.9021
240 RPQ 0.9021
241 5RO 0.9021
242 TOF 0.9020
243 I1N 0.9018
244 LKA 0.9018
245 2H5 0.9018
246 GCW 0.9015
247 7HQ 0.9015
248 C2U 0.9013
249 APZ 0.9012
250 CTS 0.9011
251 4XH 0.9011
252 M3S 0.9010
253 1U1 0.9009
254 948 0.9008
255 BTE 0.9008
256 NID 0.9008
257 AZG 0.9006
258 18N 0.9006
259 F1A 0.9005
260 M5N 0.9004
261 BOA 0.9003
262 WOO 0.9003
263 HQD 0.9003
264 3MA 0.9001
265 RAM 0.8999
266 7B4 0.8995
267 NOY 0.8995
268 INE 0.8994
269 ASO 0.8992
270 1X7 0.8991
271 JKE 0.8991
272 LI6 0.8990
273 AMG 0.8989
274 0P6 0.8988
275 FLV 0.8985
276 2KA 0.8980
277 ICT 0.8979
278 MAN 0.8975
279 ADE 0.8974
280 PA1 0.8973
281 5CU 0.8973
282 GTL 0.8970
283 IFL 0.8969
284 JIF 0.8968
285 6GU 0.8967
286 HKD 0.8967
287 4SV 0.8966
288 FPK 0.8966
289 CN0 0.8964
290 5RN 0.8964
291 NCD 0.8963
292 LZ2 0.8962
293 YH7 0.8962
294 DIU 0.8961
295 AHR 0.8960
296 SOE 0.8960
297 FA0 0.8960
298 MO8 0.8959
299 KIB 0.8957
300 BMA 0.8957
301 PRZ 0.8956
302 1GN 0.8954
303 VNJ 0.8954
304 EA1 0.8952
305 IBM 0.8951
306 LT8 0.8951
307 D07 0.8949
308 2FG 0.8948
309 DRL 0.8948
310 BK9 0.8945
311 GLA 0.8945
312 67N 0.8944
313 HPA 0.8944
314 1WD 0.8943
315 7HP 0.8942
316 FBV 0.8941
317 HH5 0.8940
318 F3B 0.8938
319 7W1 0.8938
320 AJV 0.8937
321 F81 0.8936
322 SYA 0.8933
323 XQG 0.8933
324 7WV 0.8933
325 12Q 0.8930
326 JXN 0.8930
327 NVU 0.8930
328 DIE 0.8929
329 Q77 0.8927
330 SWD 0.8927
331 ALL 0.8923
332 JFD 0.8923
333 0N7 0.8923
334 8CM 0.8922
335 DBX 0.8922
336 KBB 0.8922
337 5QX 0.8921
338 TTL 0.8921
339 DOB 0.8920
340 226 0.8919
341 9HX 0.8917
342 GLT 0.8916
343 ICO 0.8916
344 9DA 0.8914
345 1U6 0.8913
346 7MH 0.8913
347 CWS 0.8911
348 94B 0.8910
349 EYK 0.8910
350 KYD 0.8908
351 HQT 0.8908
352 M1E 0.8907
353 QM1 0.8906
354 KJ5 0.8903
355 O72 0.8903
356 URC 0.8899
357 5CL 0.8898
358 6MP 0.8897
359 5NU 0.8897
360 7WA 0.8894
361 3Z8 0.8892
362 091 0.8891
363 23J 0.8890
364 0CU 0.8890
365 5MK 0.8889
366 82I 0.8888
367 3DM 0.8887
368 ADA 0.8884
369 209 0.8884
370 6VD 0.8882
371 BP1 0.8882
372 MUA 0.8882
373 GV9 0.8879
374 M1A 0.8879
375 12M 0.8878
376 MIG 0.8878
377 GXL 0.8877
378 4M0 0.8876
379 SR4 0.8875
380 RNS 0.8874
381 Z5P 0.8872
382 KUF 0.8872
383 VNL 0.8871
384 4Z4 0.8869
385 IPM 0.8869
386 CKX 0.8867
387 P3K 0.8866
388 2LY 0.8866
389 A7W 0.8866
390 B55 0.8866
391 GIV 0.8865
392 KIA 0.8863
393 KT7 0.8862
394 MMA 0.8858
395 G4D 0.8857
396 RM4 0.8856
397 YIO 0.8854
398 QX4 0.8854
399 XHP 0.8852
400 X6X 0.8851
401 KJH 0.8849
402 B62 0.8849
403 MFB 0.8848
404 BEA 0.8847
405 SWA 0.8845
406 7A3 0.8845
407 SOR 0.8844
408 LZM 0.8843
409 0LH 0.8843
410 HA7 0.8841
411 SKA 0.8841
412 2CL 0.8840
413 ORO 0.8839
414 BCP 0.8838
415 FHN 0.8837
416 K2P 0.8837
417 K17 0.8835
418 DQU 0.8833
419 8IG 0.8833
420 4XV 0.8831
421 K3Q 0.8831
422 T6C 0.8831
423 10L 0.8830
424 FCB 0.8830
425 SX1 0.8829
426 FB1 0.8829
427 FUF 0.8827
428 H33 0.8826
429 3DO 0.8826
430 Q88 0.8826
431 BDF 0.8825
432 F05 0.8825
433 CIT 0.8825
434 FSW 0.8824
435 ISN 0.8823
436 NLA 0.8823
437 260 0.8823
438 LCN 0.8823
439 4MU 0.8822
440 X05 0.8821
441 B0D 0.8820
442 AUD 0.8819
443 PM6 0.8819
444 3RI 0.8814
445 V6F 0.8813
446 RHU 0.8813
447 0FO 0.8811
448 ES4 0.8808
449 AFR 0.8806
450 JZ3 0.8805
451 35C 0.8804
452 M2K 0.8803
453 BHA 0.8802
454 TBS 0.8802
455 QBK 0.8800
456 GAF 0.8799
457 42A 0.8799
458 7D2 0.8798
459 H6B 0.8798
460 RM1 0.8797
461 DMJ 0.8796
462 CLZ 0.8794
463 CBF 0.8793
464 FH2 0.8793
465 34D 0.8791
466 DOR 0.8790
467 A65 0.8790
468 67X 0.8788
469 B5D 0.8788
470 FCA 0.8787
471 SHA 0.8786
472 9EW 0.8785
473 FA3 0.8783
474 ES0 0.8782
475 V55 0.8782
476 8TX 0.8782
477 1WG 0.8782
478 DQA 0.8779
479 MRW 0.8779
480 HLR 0.8778
481 QIC 0.8778
482 FLC 0.8775
483 PHH 0.8775
484 GDE 0.8774
485 7CT 0.8772
486 7WR 0.8772
487 6XI 0.8772
488 BTY 0.8768
489 MFU 0.8768
490 MT5 0.8767
491 ZWZ 0.8766
492 4PW 0.8764
493 FRU 0.8761
494 PFL 0.8760
495 SYG 0.8760
496 2D0 0.8759
497 0RW 0.8758
498 6M9 0.8756
499 44W 0.8755
500 S3B 0.8754
501 1P7 0.8752
502 FP1 0.8752
503 3TJ 0.8751
504 FGZ 0.8750
505 24B 0.8750
506 SVD 0.8749
507 FDK 0.8746
508 92K 0.8746
509 FA6 0.8745
510 T9G 0.8745
511 3XX 0.8743
512 GXY 0.8742
513 D1X 0.8741
514 75K 0.8740
515 DIN 0.8740
516 X8D 0.8738
517 4XS 0.8737
518 3Z7 0.8737
519 X09 0.8736
520 ZB1 0.8735
521 DNC 0.8734
522 4AN 0.8734
523 IV2 0.8731
524 OTW 0.8731
525 39U 0.8730
526 44V 0.8730
527 IPB 0.8729
528 GLF 0.8729
529 COU 0.8728
530 GYP 0.8727
531 KKN 0.8725
532 7W4 0.8724
533 I6G 0.8720
534 F12 0.8716
535 GOO 0.8716
536 MVN 0.8712
537 FYU 0.8711
538 MSN 0.8709
539 JU2 0.8709
540 CWM 0.8709
541 HMU 0.8707
542 UFV 0.8702
543 4M4 0.8702
544 TRA 0.8701
545 293 0.8700
546 R8A 0.8700
547 MA3 0.8697
548 NK 0.8695
549 SKM 0.8695
550 XQ0 0.8694
551 JXW 0.8694
552 HMH 0.8693
553 ASC 0.8691
554 KP6 0.8691
555 9KH 0.8689
556 6LW 0.8689
557 150 0.8689
558 NDH 0.8686
559 OCH 0.8682
560 DHB 0.8680
561 1DW 0.8677
562 TAG 0.8677
563 1KP 0.8676
564 0TR 0.8673
565 5JQ 0.8672
566 6ME 0.8672
567 M6N 0.8672
568 OXC 0.8668
569 LYL 0.8668
570 C2Y 0.8667
571 KIF 0.8667
572 57O 0.8667
573 4KL 0.8661
574 MNM 0.8658
575 TQU 0.8657
576 BRV 0.8653
577 1LN 0.8652
578 2AK 0.8649
579 A13 0.8646
580 PYG 0.8645
581 GLY PRO 0.8640
582 GMN 0.8639
583 QSH 0.8637
584 N8Y 0.8635
585 JZ1 0.8634
586 MBD 0.8634
587 5JL 0.8632
588 286 0.8632
589 0R0 0.8628
590 6BL 0.8627
591 3R6 0.8626
592 ARP 0.8625
593 LT2 0.8625
594 MS9 0.8621
595 2LP 0.8619
596 XAZ 0.8617
597 3R9 0.8616
598 1FF 0.8615
599 ODO 0.8614
600 CDV 0.8612
601 H62 0.8611
602 RIB 0.8607
603 261 0.8606
604 ZXD 0.8605
605 3MH 0.8601
606 ES5 0.8600
607 L46 0.8598
608 TSS 0.8594
609 J9Q 0.8589
610 2A7 0.8583
611 TBP 0.8581
612 JZ4 0.8579
613 K32 0.8579
614 4TU 0.8577
615 4TE 0.8575
616 UFO 0.8568
617 S76 0.8567
618 NGO 0.8561
619 PQK 0.8554
620 2FY 0.8550
621 3CE 0.8549
622 9BZ 0.8548
623 LAO 0.8547
624 FLM 0.8547
625 4JT 0.8538
626 TM4 0.8530
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6DJJ; Ligand: GM7; 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: 6djj.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6DJJ; Ligand: GM7; 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: 6djj.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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