Receptor
PDB id Resolution Class Description Source Keywords
6DIE 1.78 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH Z FRAGMENT BENZENE-1,2,4-TRICARBOXYLIC ACID FROM SINGLE SOAK 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:703;
B:702;
A:702;
B:703;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GHM B:701;
A:701;
Valid;
Valid;
none;
none;
ic50 = 0.74 mM
210.14 C9 H6 O6 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: GHM; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 GHM 1 1
2 12T 0.5 0.615385
3 GJS 0.444444 0.8
4 GM7 0.432432 0.666667
5 8G0 0.424242 0.875
6 PHT 0.419355 1
7 DHB 0.416667 0.681818
8 PMA 0.413793 1
9 NDD 0.4 0.7
Similar Ligands (3D)
Ligand no: 1; Ligand: GHM; Similar ligands found: 425
No: Ligand Similarity coefficient
1 4NO 0.9530
2 TWO 0.9485
3 IL5 0.9419
4 2K8 0.9382
5 0FK 0.9354
6 DNF 0.9346
7 V1T 0.9314
8 8HC 0.9313
9 KTW 0.9300
10 8NX 0.9299
11 SG2 0.9296
12 QAT 0.9295
13 UFO 0.9287
14 HHS 0.9286
15 6R8 0.9262
16 NAG 0.9261
17 N8Y 0.9224
18 ESI 0.9221
19 7I2 0.9219
20 0W1 0.9215
21 20J 0.9199
22 5TY 0.9199
23 JG8 0.9194
24 GF4 0.9186
25 AY4 0.9184
26 VNL 0.9183
27 Q71 0.9180
28 PH2 0.9178
29 ZYR 0.9172
30 GZ8 0.9170
31 QX4 0.9166
32 4KL 0.9159
33 JP2 0.9151
34 344 0.9146
35 HA5 0.9144
36 MB1 0.9143
37 8WO 0.9142
38 VXX 0.9141
39 5RO 0.9138
40 YQA 0.9127
41 ST1 0.9127
42 QAS 0.9120
43 2FQ 0.9114
44 0FO 0.9113
45 FDR 0.9111
46 DNC 0.9105
47 HHR 0.9099
48 F31 0.9078
49 KYA 0.9076
50 C8O 0.9071
51 6ME 0.9070
52 Q77 0.9069
53 DQU 0.9068
54 0JD 0.9067
55 I7C 0.9067
56 AX3 0.9066
57 WUB 0.9064
58 BZJ 0.9063
59 6QF 0.9063
60 R9Y 0.9062
61 B5D 0.9061
62 XHP 0.9058
63 68A 0.9058
64 9ZE 0.9057
65 8WT 0.9057
66 549 0.9057
67 8W9 0.9055
68 EXD 0.9051
69 HBO 0.9048
70 15N 0.9048
71 DNA 0.9044
72 F2W 0.9034
73 5VJ 0.9033
74 GNM 0.9033
75 JR2 0.9032
76 B62 0.9031
77 7WR 0.9029
78 2JK 0.9025
79 PQK 0.9021
80 BPU 0.9021
81 VOH 0.9021
82 8XQ 0.9018
83 E1T 0.9016
84 EJZ 0.9015
85 3Y7 0.9014
86 MOK 0.9010
87 K3Q 0.9008
88 44V 0.9007
89 N2M 0.9004
90 X0W 0.9003
91 BPY 0.9003
92 K97 0.9002
93 JF1 0.9001
94 OTW 0.9000
95 209 0.8997
96 ANC 0.8996
97 MVN 0.8991
98 4AV 0.8991
99 JF2 0.8988
100 BZE 0.8987
101 JND 0.8986
102 KT7 0.8986
103 H5B 0.8982
104 44W 0.8981
105 54X 0.8981
106 URC 0.8980
107 XM5 0.8977
108 JTA 0.8975
109 C9E 0.8974
110 B56 0.8974
111 692 0.8974
112 DK1 0.8972
113 SXS 0.8971
114 4ME 0.8971
115 QBK 0.8970
116 OSB 0.8965
117 ZYQ 0.8964
118 3J8 0.8964
119 QQQ 0.8961
120 1Z8 0.8954
121 4MU 0.8952
122 SLS 0.8948
123 2GQ 0.8947
124 BEA 0.8944
125 FF2 0.8943
126 537 0.8941
127 CWS 0.8938
128 8TX 0.8937
129 N7I 0.8936
130 KUF 0.8935
131 APZ 0.8934
132 NBG 0.8934
133 DPT 0.8928
134 CNI 0.8924
135 XQK 0.8923
136 9AP 0.8920
137 S60 0.8918
138 4A5 0.8915
139 GNV 0.8914
140 LDR 0.8912
141 0N7 0.8907
142 HNQ 0.8907
143 CH9 0.8902
144 TIY 0.8902
145 L46 0.8900
146 9FE 0.8900
147 DNQ 0.8900
148 MWP 0.8899
149 DIN 0.8898
150 39U 0.8897
151 GI3 0.8897
152 B55 0.8891
153 2O6 0.8889
154 BGU 0.8889
155 2EC 0.8884
156 R6T 0.8883
157 TNG 0.8881
158 N0Z 0.8877
159 JTH 0.8876
160 V55 0.8874
161 0P6 0.8874
162 APS 0.8872
163 M1Z 0.8869
164 CLZ 0.8869
165 ST4 0.8865
166 64C 0.8865
167 3Z8 0.8861
168 E35 0.8861
169 KW8 0.8857
170 0XT 0.8856
171 GNY 0.8854
172 8IG 0.8853
173 774 0.8850
174 8ZE 0.8850
175 4TU 0.8848
176 H33 0.8848
177 8MO 0.8847
178 3R6 0.8846
179 4M4 0.8845
180 XAZ 0.8845
181 ZHA 0.8843
182 BTY 0.8843
183 AJV 0.8841
184 DPZ 0.8841
185 AVR 0.8841
186 MRW 0.8839
187 M5N 0.8838
188 H4B 0.8836
189 ESP 0.8836
190 MUA 0.8834
191 27B 0.8834
192 HQD 0.8833
193 BZ2 0.8833
194 PRF 0.8833
195 8CM 0.8833
196 3TJ 0.8830
197 CHB 0.8828
198 ESX 0.8826
199 A29 0.8825
200 75K 0.8825
201 ZME 0.8822
202 7ME 0.8821
203 1HN 0.8820
204 MXD 0.8817
205 NPA 0.8816
206 HBI 0.8815
207 SKF 0.8812
208 2HC 0.8810
209 4BY 0.8809
210 39O 0.8809
211 3QV 0.8807
212 4RU 0.8805
213 1F1 0.8804
214 1X8 0.8803
215 MNS 0.8803
216 1KP 0.8802
217 GJP 0.8801
218 A7W 0.8800
219 THA 0.8799
220 ARP 0.8796
221 N2I 0.8793
222 BIO 0.8792
223 K25 0.8792
224 0HO 0.8789
225 PEY 0.8789
226 GO2 0.8788
227 R20 0.8787
228 AZ9 0.8786
229 TT4 0.8781
230 GDE 0.8781
231 XFE 0.8781
232 0HN 0.8779
233 G12 0.8779
234 AA 0.8773
235 4A3 0.8773
236 B21 0.8773
237 428 0.8773
238 BHQ 0.8771
239 CB1 0.8771
240 61M 0.8770
241 ROI 0.8770
242 2J2 0.8768
243 2D3 0.8767
244 E7S 0.8767
245 2HO 0.8767
246 9R5 0.8761
247 X11 0.8761
248 PLP 0.8759
249 INO 0.8758
250 IAC 0.8758
251 1A7 0.8757
252 EGR 0.8756
253 H05 0.8756
254 L5V 0.8755
255 JU2 0.8753
256 AEH 0.8752
257 ZSP 0.8752
258 AN3 0.8752
259 LI6 0.8752
260 8NB 0.8751
261 4BL 0.8750
262 N3W 0.8748
263 AJY 0.8747
264 1IT 0.8746
265 GSY 0.8746
266 EN1 0.8745
267 4V6 0.8744
268 6ZW 0.8744
269 78Y 0.8742
270 93K 0.8741
271 1VK 0.8741
272 5JQ 0.8740
273 P7Y 0.8740
274 HKD 0.8739
275 M6P 0.8738
276 CKU 0.8738
277 NNO 0.8737
278 HQJ 0.8735
279 5NE 0.8735
280 3HM 0.8735
281 5JL 0.8735
282 FHB 0.8732
283 F0J 0.8731
284 EV0 0.8731
285 92P 0.8731
286 X0U 0.8730
287 CR1 0.8730
288 RKV 0.8728
289 MUR 0.8728
290 3ZB 0.8727
291 9CA 0.8726
292 P9P 0.8726
293 UNJ 0.8725
294 PQ0 0.8722
295 KY3 0.8721
296 IBM 0.8720
297 I7A 0.8717
298 GZ2 0.8717
299 4NC 0.8716
300 JAW 0.8716
301 MYJ 0.8715
302 6NT 0.8714
303 FHC 0.8714
304 IHB 0.8713
305 30G 0.8713
306 293 0.8712
307 ANF 0.8711
308 IPT 0.8711
309 GO8 0.8710
310 FLV 0.8710
311 AJ2 0.8709
312 55D 0.8707
313 6RQ 0.8707
314 4JQ 0.8705
315 5WT 0.8705
316 DX1 0.8705
317 I7B 0.8702
318 QSB 0.8701
319 8WZ 0.8701
320 FOT 0.8700
321 GDL 0.8699
322 M3E 0.8698
323 BIK 0.8696
324 64E 0.8696
325 9FL 0.8695
326 97T 0.8694
327 NDM 0.8694
328 KDV 0.8694
329 3R4 0.8694
330 BA5 0.8693
331 E1K 0.8693
332 INE 0.8690
333 2AK 0.8686
334 3A9 0.8683
335 RH1 0.8682
336 ONR 0.8681
337 2A9 0.8680
338 BBK 0.8680
339 878 0.8677
340 JYB 0.8677
341 AQO 0.8676
342 CKA 0.8676
343 EUG 0.8676
344 2HQ 0.8674
345 2KA 0.8672
346 H7Y 0.8671
347 2ZM 0.8669
348 I6G 0.8669
349 X0V 0.8668
350 M78 0.8668
351 Z5P 0.8666
352 DRG 0.8665
353 N91 0.8664
354 9TW 0.8663
355 F12 0.8662
356 4HM 0.8657
357 L22 0.8656
358 KLK 0.8651
359 SYA 0.8651
360 PXL 0.8649
361 YTX 0.8645
362 PRZ 0.8644
363 QSH 0.8642
364 363 0.8642
365 M1Q 0.8640
366 67X 0.8634
367 JLZ 0.8632
368 KMY 0.8630
369 D07 0.8629
370 SX1 0.8628
371 KIB 0.8627
372 EMZ 0.8624
373 2CZ 0.8623
374 1QP 0.8623
375 4M0 0.8622
376 GNJ 0.8620
377 2D0 0.8620
378 5OF 0.8616
379 JDN 0.8613
380 IOS 0.8613
381 LZ2 0.8608
382 226 0.8607
383 HPT 0.8606
384 4I5 0.8604
385 NID 0.8604
386 EVF 0.8603
387 TR4 0.8599
388 CWM 0.8596
389 TGX 0.8596
390 BGP 0.8596
391 2WU 0.8595
392 MCO 0.8594
393 463 0.8592
394 ST3 0.8591
395 E7Z 0.8591
396 XDE 0.8589
397 TQU 0.8587
398 SYV 0.8582
399 CIY 0.8581
400 YO5 0.8578
401 GI1 0.8578
402 NGA 0.8577
403 K44 0.8576
404 JGB 0.8571
405 5GT 0.8569
406 J9T 0.8569
407 9KZ 0.8564
408 ST2 0.8561
409 ES0 0.8560
410 KF5 0.8558
411 6FZ 0.8557
412 GO1 0.8552
413 S7J 0.8551
414 S98 0.8550
415 AC2 0.8547
416 2UZ 0.8546
417 KWH 0.8542
418 1U1 0.8538
419 4FH 0.8538
420 MS9 0.8534
421 6HP 0.8531
422 5PX 0.8531
423 36E 0.8525
424 LNR 0.8516
425 4XV 0.8515
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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