Receptor
PDB id Resolution Class Description Source Keywords
6MJ5 1.85 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ519 HOMO SAPIENS FRAGMENT BASED DRUG DESIGN ANTI-CANCER DRUG DESIGN DNA BINPROTEIN 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:703;
A:701;
B:702;
A:702;
B:701;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
JTA B:703;
A:704;
 Valid;
Valid;
 none;
none;
 submit data
234.165 C10 H6 N2 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: JTA; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 JTA 1 1
2 GNV 0.576923 0.66
3 GNY 0.534483 0.603774
Similar Ligands (3D)
Ligand no: 1; Ligand: JTA; Similar ligands found: 471
No: Ligand Similarity coefficient
1 GNJ 0.9716
2 GNM 0.9499
3 JP2 0.9449
4 30G 0.9449
5 344 0.9447
6 NRA 0.9356
7 9TF 0.9344
8 2JK 0.9335
9 S60 0.9323
10 5F8 0.9319
11 DRG 0.9308
12 DPT 0.9307
13 JRO 0.9306
14 537 0.9298
15 6QF 0.9288
16 WUB 0.9288
17 ANC 0.9287
18 7I2 0.9277
19 1X8 0.9265
20 DK1 0.9260
21 BGU 0.9260
22 3J8 0.9259
23 TCR 0.9256
24 ZSP 0.9250
25 LL1 0.9248
26 NAG 0.9247
27 BA5 0.9240
28 H4B 0.9240
29 F40 0.9238
30 ALR 0.9238
31 TIY 0.9237
32 KW8 0.9233
33 YE7 0.9232
34 II4 0.9230
35 BIK 0.9229
36 XM5 0.9228
37 THA 0.9227
38 CKA 0.9226
39 2GQ 0.9224
40 CNI 0.9221
41 LP8 0.9221
42 3Y7 0.9220
43 F2W 0.9216
44 54X 0.9212
45 BPU 0.9212
46 774 0.9212
47 AA 0.9211
48 ANF 0.9206
49 LDR 0.9205
50 9AP 0.9204
51 5TY 0.9203
52 MNX 0.9202
53 IQZ 0.9201
54 DNQ 0.9197
55 HBO 0.9195
56 8G6 0.9193
57 0XT 0.9185
58 JG8 0.9185
59 DXK 0.9181
60 68A 0.9177
61 AMR 0.9171
62 EMO 0.9170
63 27M 0.9169
64 5V7 0.9167
65 B21 0.9163
66 FQX 0.9162
67 5FL 0.9160
68 E1K 0.9158
69 P9I 0.9157
70 V1T 0.9157
71 EWG 0.9148
72 VM1 0.9146
73 ZME 0.9145
74 5WT 0.9142
75 LUM 0.9136
76 TXQ 0.9135
77 HRM 0.9127
78 PRL 0.9126
79 BPY 0.9122
80 0LO 0.9117
81 DX1 0.9113
82 9CE 0.9105
83 8NX 0.9096
84 9UL 0.9093
85 2K8 0.9093
86 6FB 0.9092
87 CZ0 0.9091
88 H5B 0.9087
89 6TJ 0.9085
90 MS0 0.9082
91 BZJ 0.9082
92 X11 0.9077
93 2J2 0.9059
94 HNA 0.9054
95 OCZ 0.9054
96 78Y 0.9054
97 6ZW 0.9048
98 1V3 0.9046
99 CHQ 0.9041
100 TXW 0.9037
101 64E 0.9036
102 AVA 0.9034
103 5TZ 0.9032
104 YO5 0.9031
105 LEL 0.9027
106 DX3 0.9026
107 3QV 0.9025
108 582 0.9024
109 M5H 0.9020
110 R9Y 0.9018
111 549 0.9017
112 4MU 0.9016
113 64C 0.9016
114 4FF 0.9015
115 19E 0.9013
116 AJY 0.9011
117 PEY 0.9010
118 M3E 0.9010
119 49P 0.9009
120 BZE 0.9007
121 C8O 0.9005
122 HHS 0.9005
123 K68 0.9003
124 67X 0.9002
125 AN3 0.9001
126 L3L 0.8998
127 N0Z 0.8998
128 CX6 0.8997
129 ROI 0.8991
130 LF5 0.8990
131 IQ5 0.8988
132 NDG 0.8987
133 982 0.8983
134 L07 0.8983
135 7MX 0.8983
136 K44 0.8982
137 5GT 0.8981
138 5VJ 0.8981
139 AY4 0.8980
140 XFE 0.8977
141 GHM 0.8975
142 1KP 0.8974
143 39Z 0.8974
144 1HN 0.8973
145 JR2 0.8973
146 5NN 0.8972
147 FDR 0.8972
148 RVE 0.8971
149 1QP 0.8968
150 ZYR 0.8967
151 BIO 0.8964
152 QR2 0.8964
153 X0W 0.8964
154 GJP 0.8959
155 DX7 0.8958
156 1YL 0.8957
157 2WU 0.8957
158 ITE 0.8956
159 5F5 0.8954
160 RGK 0.8951
161 SG2 0.8950
162 EV2 0.8943
163 P4L 0.8942
164 CLZ 0.8940
165 WS7 0.8939
166 1EL 0.8939
167 N2M 0.8938
168 GDL 0.8935
169 226 0.8932
170 AH3 0.8932
171 G12 0.8925
172 K25 0.8925
173 FCD 0.8924
174 6X9 0.8924
175 FLV 0.8923
176 SRO 0.8920
177 S98 0.8920
178 0FR 0.8919
179 LFQ 0.8919
180 C9E 0.8916
181 8MO 0.8916
182 LFN 0.8914
183 WLH 0.8913
184 A73 0.8911
185 5P3 0.8911
186 2FQ 0.8909
187 U7E 0.8907
188 7FF 0.8903
189 28N 0.8903
190 1DR 0.8902
191 CSN 0.8901
192 PH2 0.8897
193 4KL 0.8897
194 4TU 0.8896
195 7B3 0.8895
196 X0U 0.8894
197 1V1 0.8892
198 A5H 0.8888
199 3R4 0.8887
200 AH9 0.8886
201 MNY 0.8886
202 4BL 0.8885
203 OAI 0.8884
204 YE6 0.8883
205 GF4 0.8882
206 HA6 0.8881
207 CK2 0.8880
208 KCH 0.8879
209 WS6 0.8878
210 E7S 0.8878
211 1AJ 0.8876
212 4AU 0.8875
213 7L4 0.8874
214 1A7 0.8873
215 HRD 0.8872
216 ZHA 0.8870
217 MUR 0.8867
218 E1T 0.8867
219 L22 0.8867
220 2J1 0.8866
221 CUE 0.8865
222 IL5 0.8864
223 3D8 0.8863
224 HA5 0.8863
225 363 0.8859
226 0FK 0.8859
227 9KZ 0.8858
228 20D 0.8858
229 4BY 0.8855
230 1QV 0.8855
231 18E 0.8854
232 KMY 0.8852
233 27B 0.8851
234 F5C 0.8851
235 TRP 0.8851
236 0W1 0.8850
237 3VX 0.8849
238 UFO 0.8849
239 V2Z 0.8847
240 2LW 0.8844
241 692 0.8844
242 YZ9 0.8843
243 QMS 0.8842
244 4RU 0.8840
245 3C5 0.8840
246 N91 0.8840
247 KYA 0.8838
248 KLV 0.8837
249 DNA 0.8836
250 4G2 0.8835
251 ESI 0.8834
252 5E5 0.8831
253 JY4 0.8829
254 JCZ 0.8827
255 CCV 0.8826
256 15N 0.8822
257 8W9 0.8818
258 0JD 0.8816
259 DNF 0.8816
260 GI3 0.8816
261 LOG 0.8815
262 BBY 0.8815
263 JWS 0.8814
264 2D2 0.8813
265 M3F 0.8810
266 NOM 0.8809
267 DFL 0.8808
268 1VK 0.8806
269 JYB 0.8805
270 4V2 0.8796
271 4I8 0.8795
272 KYN 0.8795
273 6KT 0.8794
274 8HC 0.8794
275 JF8 0.8793
276 1V4 0.8793
277 0UL 0.8793
278 4NO 0.8792
279 NBG 0.8789
280 6E8 0.8788
281 I6G 0.8786
282 5NE 0.8784
283 8NB 0.8782
284 TWO 0.8782
285 12T 0.8781
286 25F 0.8778
287 MXD 0.8778
288 C09 0.8777
289 P83 0.8777
290 55D 0.8776
291 9R5 0.8776
292 Y3L 0.8776
293 G6P 0.8775
294 KTW 0.8775
295 JND 0.8774
296 0SY 0.8774
297 3GX 0.8769
298 VUP 0.8769
299 5GV 0.8766
300 9CA 0.8763
301 39O 0.8763
302 YTX 0.8763
303 1ZC 0.8763
304 S62 0.8762
305 NLA 0.8762
306 0J4 0.8761
307 0N7 0.8761
308 X8D 0.8761
309 0F9 0.8760
310 3ZB 0.8759
311 0J2 0.8758
312 HQD 0.8758
313 8WZ 0.8757
314 FER 0.8753
315 K7H 0.8753
316 428 0.8752
317 209 0.8752
318 YEX 0.8751
319 AH6 0.8750
320 9FE 0.8746
321 AO6 0.8745
322 JU2 0.8745
323 UXH 0.8745
324 QX4 0.8741
325 ZRK 0.8741
326 78P 0.8740
327 JGB 0.8740
328 1IT 0.8740
329 CB1 0.8740
330 64F 0.8738
331 15E 0.8737
332 ZYQ 0.8736
333 NYJ 0.8735
334 D87 0.8735
335 4GU 0.8735
336 JBZ 0.8733
337 ET0 0.8731
338 XEZ 0.8731
339 DQU 0.8731
340 1X7 0.8729
341 9OF 0.8729
342 5RO 0.8729
343 X48 0.8728
344 I7B 0.8728
345 PMP 0.8728
346 T28 0.8727
347 0OK 0.8724
348 HC8 0.8722
349 BG6 0.8721
350 HBI 0.8720
351 VXX 0.8718
352 9ZE 0.8717
353 9FL 0.8717
354 0FO 0.8715
355 2D3 0.8715
356 TOF 0.8710
357 B4O 0.8709
358 DT7 0.8706
359 EY2 0.8706
360 F95 0.8705
361 G1P 0.8704
362 2O6 0.8702
363 4F8 0.8702
364 DBF 0.8702
365 J38 0.8701
366 X0T 0.8701
367 2LY 0.8701
368 K48 0.8699
369 44V 0.8697
370 8HH 0.8696
371 D80 0.8695
372 A6W 0.8694
373 Z21 0.8691
374 KJU 0.8689
375 Q5M 0.8689
376 U19 0.8688
377 DBQ 0.8687
378 GI1 0.8684
379 5AD 0.8684
380 AXX 0.8683
381 EXD 0.8683
382 H05 0.8682
383 MT8 0.8682
384 D3G 0.8680
385 PUE 0.8678
386 6DQ 0.8677
387 6ME 0.8675
388 92P 0.8672
389 0SX 0.8668
390 C2Y 0.8667
391 QIV 0.8666
392 K3Q 0.8662
393 R6T 0.8661
394 NEU 0.8660
395 PQ0 0.8659
396 FF2 0.8658
397 N8Y 0.8657
398 Q8G 0.8656
399 XG1 0.8655
400 RH1 0.8655
401 4AN 0.8654
402 3SU 0.8653
403 SKF 0.8653
404 DUR 0.8650
405 5NS 0.8648
406 BGP 0.8646
407 AJV 0.8645
408 FSU 0.8644
409 HHR 0.8644
410 UNJ 0.8644
411 MD6 0.8642
412 L1T 0.8639
413 ONR 0.8639
414 CIY 0.8639
415 M6Z 0.8637
416 8XQ 0.8637
417 IPD 0.8635
418 WSD 0.8632
419 HQJ 0.8630
420 9F8 0.8629
421 SZ5 0.8628
422 FUJ 0.8628
423 N7I 0.8624
424 5XL 0.8621
425 EV3 0.8618
426 795 0.8617
427 MXX 0.8616
428 LOT 0.8615
429 S0E 0.8613
430 3F4 0.8612
431 2KA 0.8610
432 39U 0.8610
433 THM 0.8606
434 K37 0.8602
435 6J9 0.8599
436 PQK 0.8597
437 LZ2 0.8596
438 57D 0.8594
439 5GU 0.8594
440 I7C 0.8592
441 1FE 0.8586
442 NPL 0.8585
443 LDC 0.8584
444 5WS 0.8572
445 APZ 0.8571
446 61M 0.8569
447 SU9 0.8569
448 TR4 0.8567
449 L5V 0.8566
450 8TX 0.8566
451 LWS 0.8565
452 NGA 0.8565
453 QQQ 0.8557
454 DIN 0.8556
455 AZN 0.8555
456 NWD 0.8554
457 DT9 0.8554
458 ARP 0.8544
459 SYA 0.8540
460 MN QAY 0.8540
461 4XF 0.8539
462 AJ1 0.8539
463 878 0.8537
464 GZ2 0.8536
465 25O 0.8535
466 GJK 0.8530
467 MRW 0.8529
468 LJW 0.8526
469 KU1 0.8525
470 4VY 0.8517
471 APS 0.8513
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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