Receptor
PDB id Resolution Class Description Source Keywords
6DJF 1.67 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ502 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 A:701;
B:702;
B:703;
B:701;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GNV A:702;
B:704;
Valid;
Valid;
none;
none;
submit data
233.177 C11 H7 N O5 c1cc2...
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: GNV; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 GNV 1 1
2 GNJ 0.6 0.622642
3 JTA 0.576923 0.66
4 GNY 0.566038 0.888889
5 GJP 0.461538 0.939394
6 DBH 0.4 0.6
Similar Ligands (3D)
Ligand no: 1; Ligand: GNV; Similar ligands found: 550
No: Ligand Similarity coefficient
1 GNM 0.9547
2 JP2 0.9484
3 30G 0.9437
4 WUB 0.9433
5 344 0.9415
6 2JK 0.9377
7 NRA 0.9350
8 5F8 0.9334
9 9TF 0.9333
10 CNI 0.9314
11 JRO 0.9299
12 S60 0.9295
13 KW8 0.9291
14 DRG 0.9290
15 DK1 0.9278
16 BGU 0.9271
17 1X8 0.9269
18 DPT 0.9268
19 5TZ 0.9266
20 537 0.9265
21 6QF 0.9263
22 ANC 0.9261
23 7I2 0.9256
24 TCR 0.9247
25 YE7 0.9244
26 CKA 0.9244
27 MS0 0.9243
28 3J8 0.9239
29 XM5 0.9239
30 LL1 0.9237
31 NAG 0.9233
32 F40 0.9233
33 IQ5 0.9231
34 AVA 0.9228
35 ZSP 0.9227
36 II4 0.9226
37 DNQ 0.9222
38 OCZ 0.9222
39 549 0.9222
40 KWH 0.9217
41 H4B 0.9217
42 BA5 0.9216
43 ALR 0.9214
44 BIK 0.9214
45 774 0.9212
46 F2W 0.9211
47 LP8 0.9207
48 THA 0.9207
49 2GQ 0.9207
50 TIY 0.9206
51 MNX 0.9204
52 3Y7 0.9201
53 9AP 0.9196
54 LDR 0.9193
55 AA 0.9189
56 ANF 0.9184
57 IQZ 0.9184
58 0XT 0.9179
59 BPU 0.9179
60 54X 0.9178
61 5TY 0.9178
62 8G6 0.9176
63 27M 0.9175
64 P9I 0.9173
65 5FL 0.9173
66 AMR 0.9169
67 DXK 0.9167
68 EMO 0.9161
69 JG8 0.9158
70 68A 0.9157
71 8NX 0.9156
72 EWG 0.9153
73 HBO 0.9152
74 2J2 0.9152
75 5V7 0.9152
76 982 0.9145
77 B21 0.9144
78 VM1 0.9137
79 E1K 0.9134
80 V1T 0.9133
81 PRL 0.9130
82 HRM 0.9129
83 5WT 0.9129
84 YO5 0.9126
85 TXQ 0.9126
86 LUM 0.9117
87 6TJ 0.9115
88 0LO 0.9113
89 FCD 0.9110
90 ZME 0.9109
91 9CE 0.9103
92 49P 0.9094
93 BPY 0.9094
94 7L4 0.9093
95 CZ0 0.9088
96 LF5 0.9088
97 78Y 0.9084
98 TXW 0.9084
99 FQX 0.9082
100 6FB 0.9080
101 RVE 0.9070
102 H5B 0.9069
103 C8O 0.9067
104 9UL 0.9065
105 2K8 0.9064
106 BZJ 0.9063
107 5F5 0.9062
108 67X 0.9058
109 1YL 0.9052
110 HNA 0.9050
111 KCH 0.9048
112 1V3 0.9046
113 DX1 0.9046
114 ITE 0.9038
115 6ZW 0.9033
116 64E 0.9033
117 1FL 0.9029
118 CHQ 0.9028
119 3QV 0.9021
120 582 0.9021
121 DX3 0.9020
122 19E 0.9019
123 4FF 0.9017
124 LEL 0.9015
125 64C 0.9013
126 4I5 0.9011
127 6X9 0.9009
128 5OF 0.9009
129 4MU 0.9008
130 X11 0.9007
131 1KP 0.9006
132 K68 0.9004
133 R9Y 0.9003
134 EV2 0.9002
135 5VJ 0.9001
136 M5H 0.9000
137 AJY 0.8999
138 K44 0.8996
139 U7E 0.8995
140 L3L 0.8994
141 P4L 0.8993
142 7FF 0.8992
143 BQ5 0.8992
144 NDG 0.8990
145 AH3 0.8988
146 N0Z 0.8986
147 L07 0.8985
148 PEY 0.8979
149 BZE 0.8979
150 HHS 0.8977
151 X0W 0.8976
152 CX6 0.8975
153 3C5 0.8972
154 DX7 0.8972
155 5NN 0.8969
156 AY4 0.8969
157 ROI 0.8966
158 2WU 0.8961
159 AN3 0.8961
160 SG2 0.8960
161 39Z 0.8959
162 V2Z 0.8955
163 SSY 0.8954
164 5E5 0.8954
165 FDR 0.8953
166 RKV 0.8953
167 HA6 0.8952
168 4AU 0.8952
169 AH9 0.8945
170 JR2 0.8945
171 XFE 0.8945
172 RGK 0.8945
173 YZ9 0.8943
174 3R4 0.8942
175 1EL 0.8942
176 LFQ 0.8940
177 7MX 0.8940
178 1HN 0.8938
179 ZHA 0.8935
180 K25 0.8934
181 1QP 0.8929
182 1QV 0.8929
183 GDL 0.8927
184 ZYR 0.8927
185 NKI 0.8927
186 OAI 0.8926
187 FLV 0.8923
188 WS7 0.8923
189 226 0.8920
190 J1K 0.8919
191 G12 0.8919
192 1AJ 0.8919
193 9KZ 0.8918
194 CLZ 0.8916
195 BIO 0.8915
196 QR2 0.8915
197 N2M 0.8915
198 IL5 0.8914
199 GHM 0.8914
200 VKE 0.8912
201 A73 0.8911
202 7B3 0.8909
203 S98 0.8908
204 WLH 0.8908
205 JF8 0.8907
206 IDZ 0.8905
207 5P3 0.8905
208 MUR 0.8904
209 LOG 0.8904
210 JBZ 0.8900
211 0FR 0.8898
212 LFN 0.8898
213 SRO 0.8897
214 PH2 0.8896
215 CSN 0.8896
216 GF4 0.8896
217 1DR 0.8892
218 1V1 0.8889
219 8MO 0.8889
220 2D2 0.8886
221 2FQ 0.8886
222 4KL 0.8884
223 4TU 0.8883
224 C9E 0.8882
225 YE6 0.8882
226 AO6 0.8881
227 CUE 0.8881
228 KWB 0.8880
229 UN9 0.8877
230 HRD 0.8875
231 5GT 0.8874
232 692 0.8873
233 28N 0.8873
234 MNY 0.8873
235 NOM 0.8871
236 HBI 0.8871
237 A5H 0.8871
238 X0U 0.8871
239 6E8 0.8871
240 E7S 0.8871
241 EVO 0.8869
242 EV3 0.8867
243 4BL 0.8866
244 18E 0.8866
245 2J1 0.8862
246 CK2 0.8861
247 0J4 0.8860
248 NBG 0.8856
249 DNA 0.8856
250 M3E 0.8852
251 P83 0.8849
252 78P 0.8849
253 PIQ 0.8849
254 20D 0.8848
255 4BY 0.8846
256 DBF 0.8845
257 1A7 0.8844
258 3D8 0.8842
259 L22 0.8841
260 272 0.8840
261 3VX 0.8839
262 F95 0.8839
263 TRP 0.8839
264 4RV 0.8838
265 E1T 0.8838
266 HA5 0.8838
267 QMS 0.8836
268 4G2 0.8834
269 UFO 0.8832
270 KMY 0.8832
271 W8L 0.8831
272 363 0.8829
273 1ZC 0.8828
274 KLV 0.8828
275 0FK 0.8828
276 DFL 0.8827
277 4RU 0.8826
278 JWS 0.8825
279 ESI 0.8821
280 0W1 0.8818
281 0SX 0.8816
282 JY4 0.8816
283 GI3 0.8814
284 8W9 0.8812
285 F5C 0.8812
286 RHN 0.8811
287 M3F 0.8809
288 JCZ 0.8809
289 KTW 0.8808
290 0J2 0.8806
291 K97 0.8805
292 8SK 0.8805
293 CCV 0.8805
294 JYB 0.8804
295 25F 0.8804
296 3GX 0.8804
297 1V4 0.8802
298 4V2 0.8801
299 DNC 0.8800
300 2QU 0.8798
301 I6G 0.8796
302 FUJ 0.8795
303 12T 0.8795
304 9LI 0.8793
305 CDJ 0.8793
306 DNF 0.8789
307 BBY 0.8789
308 KYA 0.8787
309 C09 0.8787
310 6BL 0.8787
311 0JD 0.8786
312 EN1 0.8785
313 28S 0.8783
314 55D 0.8783
315 3ZB 0.8782
316 AH6 0.8781
317 15N 0.8781
318 KYN 0.8780
319 6KT 0.8779
320 2LW 0.8779
321 N91 0.8779
322 15E 0.8779
323 ET0 0.8778
324 TWO 0.8776
325 WS6 0.8775
326 MD6 0.8773
327 4I8 0.8771
328 D2G 0.8771
329 AJ1 0.8770
330 T28 0.8769
331 9R5 0.8769
332 0UL 0.8768
333 UXH 0.8766
334 H70 0.8766
335 H2W 0.8765
336 8HC 0.8765
337 VUP 0.8765
338 H05 0.8763
339 G6P 0.8762
340 AXX 0.8760
341 Q8G 0.8760
342 4NO 0.8759
343 QIV 0.8758
344 NLA 0.8756
345 B56 0.8756
346 27B 0.8756
347 GI1 0.8754
348 X8D 0.8754
349 EYA 0.8753
350 M6Z 0.8752
351 TIA 0.8751
352 CLI 0.8750
353 0N7 0.8750
354 0F9 0.8749
355 Y3L 0.8748
356 HQD 0.8748
357 I7B 0.8748
358 39O 0.8745
359 5XL 0.8744
360 XEZ 0.8744
361 K7H 0.8744
362 TT4 0.8743
363 9FE 0.8743
364 MXD 0.8741
365 JU2 0.8740
366 5GV 0.8740
367 X0T 0.8738
368 JGB 0.8737
369 22L 0.8737
370 209 0.8735
371 1X7 0.8735
372 ZYQ 0.8735
373 D87 0.8734
374 64F 0.8733
375 761 0.8730
376 YEX 0.8730
377 428 0.8730
378 9CA 0.8729
379 CB1 0.8729
380 AJG 0.8728
381 FER 0.8728
382 5RO 0.8725
383 PLP 0.8725
384 NYJ 0.8723
385 6VD 0.8723
386 ZRK 0.8721
387 4GU 0.8721
388 EY2 0.8721
389 2D3 0.8720
390 0SY 0.8717
391 DX2 0.8717
392 HC8 0.8717
393 8NB 0.8714
394 HH6 0.8714
395 2KA 0.8712
396 1IT 0.8712
397 VXX 0.8711
398 9OF 0.8710
399 J38 0.8710
400 1FE 0.8709
401 DQU 0.8709
402 QX4 0.8708
403 M3W 0.8708
404 Q8D 0.8707
405 S62 0.8706
406 OPA 0.8705
407 LOT 0.8703
408 TOF 0.8700
409 4HG 0.8699
410 D3G 0.8697
411 0OK 0.8696
412 3VQ 0.8696
413 A6W 0.8696
414 XI7 0.8695
415 R6T 0.8695
416 5NE 0.8695
417 57D 0.8694
418 C2Y 0.8693
419 795 0.8692
420 0FO 0.8692
421 Z21 0.8691
422 9ZE 0.8690
423 6MW 0.8689
424 878 0.8688
425 G1P 0.8688
426 B23 0.8688
427 B4O 0.8687
428 X48 0.8687
429 XHP 0.8686
430 44V 0.8685
431 9FL 0.8685
432 DT7 0.8685
433 PUE 0.8684
434 Q5M 0.8684
435 FF2 0.8683
436 KJU 0.8682
437 U19 0.8682
438 5NS 0.8680
439 8HH 0.8679
440 OTA 0.8679
441 D80 0.8679
442 GO2 0.8676
443 IBM 0.8674
444 ZZA 0.8673
445 L1T 0.8672
446 K3Q 0.8671
447 AZN 0.8670
448 3WL 0.8668
449 H33 0.8667
450 92P 0.8666
451 K37 0.8661
452 XG1 0.8660
453 EXD 0.8660
454 NIF 0.8660
455 UNJ 0.8659
456 ARP 0.8657
457 FSU 0.8656
458 2UD 0.8655
459 BRY 0.8655
460 2O6 0.8655
461 K48 0.8653
462 GNR 0.8653
463 YTX 0.8651
464 6PB 0.8650
465 PJW 0.8649
466 MN QAY 0.8649
467 PQ0 0.8648
468 N8Y 0.8647
469 39U 0.8647
470 34L 0.8642
471 MXX 0.8641
472 5SB 0.8641
473 4AN 0.8639
474 3SU 0.8637
475 BOQ 0.8637
476 AJV 0.8636
477 2LY 0.8636
478 MS9 0.8636
479 COL 0.8635
480 IOP 0.8635
481 LI6 0.8635
482 ONR 0.8633
483 HHR 0.8633
484 4F8 0.8632
485 DUR 0.8632
486 SZ5 0.8630
487 SKF 0.8628
488 E7R 0.8627
489 R20 0.8627
490 WSD 0.8626
491 3F4 0.8624
492 LJW 0.8622
493 THM 0.8621
494 LZ2 0.8620
495 ENO 0.8620
496 IPD 0.8619
497 XDE 0.8617
498 3QI 0.8614
499 XCG 0.8614
500 IXM 0.8613
501 OSB 0.8611
502 4VY 0.8607
503 AQN 0.8607
504 N7I 0.8605
505 MVN 0.8603
506 SU9 0.8603
507 ODK 0.8602
508 ZEA 0.8601
509 OTW 0.8601
510 2PW 0.8598
511 VT3 0.8598
512 S0E 0.8593
513 MRW 0.8590
514 E9L 0.8589
515 CUH 0.8588
516 9F8 0.8586
517 DCZ 0.8586
518 1XS 0.8586
519 LDC 0.8585
520 LIG 0.8585
521 DBQ 0.8584
522 P9E 0.8583
523 MT8 0.8582
524 RH1 0.8582
525 DIN 0.8580
526 MNS 0.8578
527 IK1 0.8578
528 HNT 0.8577
529 NWD 0.8576
530 NPL 0.8575
531 PQK 0.8573
532 6J9 0.8572
533 B98 0.8572
534 I7C 0.8567
535 TR4 0.8567
536 5GU 0.8563
537 A7W 0.8561
538 8DA 0.8553
539 NGA 0.8552
540 O82 0.8551
541 5WS 0.8551
542 ADN 0.8549
543 091 0.8547
544 QQQ 0.8546
545 DT9 0.8545
546 GJK 0.8539
547 75K 0.8537
548 SYA 0.8521
549 6RQ 0.8521
550 KU1 0.8517
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
APoc FAQ
Feedback