Receptor
PDB id Resolution Class Description Source Keywords
6DJE 1.71 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH S ALDRICH COMPOUND CDS010292 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;
A:701;
A:702;
B:701;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
GNY A:704;
B:702;
 Valid;
Valid;
 none;
none;
 submit data
231.247 C13 H13 N O3 CC(C)...
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: GNY; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GNY 1 1
2 GNV 0.566038 0.888889
3 JTA 0.534483 0.603774
Similar Ligands (3D)
Ligand no: 1; Ligand: GNY; Similar ligands found: 329
No: Ligand Similarity coefficient
1 GNJ 0.9630
2 GNM 0.9420
3 549 0.9324
4 CNI 0.9313
5 JP2 0.9255
6 TCR 0.9248
7 344 0.9241
8 MS0 0.9210
9 DPT 0.9179
10 KW8 0.9177
11 KWH 0.9173
12 2JK 0.9164
13 WUB 0.9153
14 DNQ 0.9143
15 0LO 0.9126
16 30G 0.9107
17 S60 0.9105
18 HRM 0.9095
19 BGU 0.9087
20 LP8 0.9082
21 NAG 0.9077
22 JG8 0.9072
23 6X9 0.9064
24 HBO 0.9054
25 DK1 0.9048
26 6QF 0.9044
27 TXW 0.9042
28 0XT 0.9034
29 EV2 0.9033
30 XM5 0.9032
31 ANC 0.9026
32 8NX 0.9024
33 F2W 0.9020
34 NRA 0.9015
35 AH3 0.9013
36 67X 0.9012
37 BIK 0.9008
38 Q8G 0.9007
39 5F8 0.9007
40 IQ5 0.9003
41 LF5 0.9001
42 3J8 0.8989
43 V1T 0.8984
44 OCZ 0.8982
45 LEL 0.8978
46 BPY 0.8978
47 78Y 0.8975
48 1KP 0.8973
49 YE6 0.8972
50 DRG 0.8972
51 GF4 0.8972
52 BA5 0.8969
53 RVE 0.8966
54 N2M 0.8964
55 2J1 0.8963
56 6FB 0.8961
57 P9I 0.8959
58 982 0.8957
59 H4B 0.8956
60 L3L 0.8955
61 HNA 0.8954
62 PRL 0.8954
63 AH9 0.8952
64 537 0.8945
65 SG2 0.8941
66 HBI 0.8937
67 GDL 0.8934
68 3C5 0.8931
69 EWG 0.8930
70 E1K 0.8923
71 THA 0.8922
72 FQX 0.8922
73 R9Y 0.8921
74 FCD 0.8921
75 GJP 0.8919
76 5GT 0.8918
77 X11 0.8915
78 3QV 0.8914
79 27B 0.8910
80 5WT 0.8909
81 6E8 0.8905
82 TIY 0.8899
83 YZ9 0.8898
84 IQZ 0.8898
85 AA 0.8898
86 ZSP 0.8894
87 68A 0.8893
88 6ZW 0.8893
89 U7E 0.8889
90 DX1 0.8889
91 1X8 0.8887
92 AJY 0.8887
93 774 0.8886
94 CKA 0.8884
95 Q8D 0.8884
96 5TZ 0.8883
97 5TY 0.8882
98 ANF 0.8878
99 2J2 0.8876
100 K97 0.8876
101 C8O 0.8876
102 7I2 0.8874
103 4MU 0.8873
104 EMO 0.8873
105 AH6 0.8871
106 6TJ 0.8870
107 N0Z 0.8870
108 V2Z 0.8869
109 4FF 0.8868
110 BPU 0.8868
111 E7S 0.8867
112 II4 0.8867
113 S62 0.8866
114 27M 0.8865
115 5FL 0.8863
116 J1K 0.8859
117 ROI 0.8857
118 GHM 0.8854
119 NDG 0.8854
120 49P 0.8853
121 KMY 0.8853
122 LL1 0.8851
123 X0W 0.8851
124 8G6 0.8847
125 BZJ 0.8847
126 8W9 0.8844
127 3Y7 0.8843
128 9TF 0.8842
129 YE7 0.8842
130 60L 0.8840
131 LUM 0.8834
132 4RU 0.8834
133 P4L 0.8833
134 3R4 0.8831
135 2GQ 0.8828
136 9KZ 0.8827
137 BIO 0.8824
138 BZE 0.8823
139 DX3 0.8819
140 L22 0.8816
141 54X 0.8815
142 2K8 0.8813
143 39Z 0.8813
144 1HN 0.8813
145 N91 0.8809
146 D3G 0.8802
147 MUR 0.8801
148 QR2 0.8800
149 S98 0.8800
150 9UL 0.8798
151 MNX 0.8796
152 CK2 0.8795
153 L1T 0.8794
154 F40 0.8792
155 AN3 0.8792
156 2WU 0.8791
157 12T 0.8790
158 4G2 0.8790
159 PH2 0.8790
160 VM1 0.8788
161 FLV 0.8786
162 0W1 0.8779
163 9CE 0.8776
164 LDR 0.8776
165 1ZC 0.8776
166 4BY 0.8775
167 9AP 0.8774
168 ALR 0.8769
169 HHS 0.8769
170 CLZ 0.8768
171 ITE 0.8767
172 4BL 0.8767
173 KLV 0.8767
174 1AJ 0.8765
175 3ZB 0.8763
176 FDR 0.8763
177 AY4 0.8763
178 HRD 0.8761
179 226 0.8757
180 4I5 0.8755
181 JRO 0.8753
182 J38 0.8752
183 4I8 0.8752
184 795 0.8749
185 UFO 0.8746
186 ZME 0.8745
187 K44 0.8744
188 5RO 0.8743
189 2D2 0.8741
190 4RV 0.8741
191 9LI 0.8740
192 CX6 0.8740
193 L07 0.8740
194 D2G 0.8739
195 TR4 0.8738
196 7B3 0.8738
197 5F5 0.8737
198 4TU 0.8736
199 9R5 0.8736
200 EV3 0.8733
201 X0T 0.8730
202 4V2 0.8730
203 CSN 0.8728
204 2FQ 0.8727
205 CCV 0.8727
206 JU2 0.8726
207 DXK 0.8726
208 5V7 0.8725
209 H5B 0.8724
210 B21 0.8724
211 2LW 0.8724
212 8NB 0.8724
213 LFN 0.8721
214 M6Z 0.8718
215 WS6 0.8718
216 ZYR 0.8716
217 X0U 0.8716
218 G12 0.8715
219 2KA 0.8713
220 CHQ 0.8713
221 1FL 0.8713
222 J6W 0.8712
223 KYA 0.8709
224 LOG 0.8708
225 15E 0.8708
226 TWO 0.8707
227 0SX 0.8707
228 DNA 0.8703
229 0FR 0.8698
230 A5H 0.8697
231 0F9 0.8694
232 SRO 0.8693
233 PEY 0.8690
234 I7B 0.8690
235 YTX 0.8689
236 TT4 0.8689
237 IL5 0.8686
238 55D 0.8685
239 4AU 0.8683
240 KCH 0.8682
241 K68 0.8682
242 AO6 0.8679
243 Y3L 0.8679
244 AMR 0.8679
245 ET0 0.8678
246 K7H 0.8678
247 ZHA 0.8676
248 KYN 0.8675
249 TOF 0.8671
250 5NE 0.8671
251 KTW 0.8668
252 I6G 0.8666
253 1YL 0.8665
254 K25 0.8661
255 SKF 0.8660
256 PQ0 0.8659
257 5GV 0.8659
258 CLI 0.8658
259 KJU 0.8657
260 SER DNF 0.8656
261 JYB 0.8654
262 DT7 0.8653
263 6KT 0.8653
264 15N 0.8652
265 AJ1 0.8644
266 TXQ 0.8642
267 6VD 0.8641
268 VXX 0.8641
269 DX7 0.8640
270 HC8 0.8637
271 4XF 0.8635
272 3XR 0.8634
273 M5H 0.8633
274 28N 0.8632
275 CWJ 0.8632
276 363 0.8630
277 MNS 0.8629
278 1A7 0.8627
279 FER 0.8626
280 3VX 0.8625
281 AJV 0.8624
282 AZN 0.8623
283 X6W 0.8621
284 QIV 0.8620
285 TRP 0.8620
286 64E 0.8619
287 A2G 0.8618
288 LFQ 0.8612
289 3QI 0.8605
290 AJG 0.8605
291 19E 0.8602
292 5GU 0.8601
293 5NS 0.8597
294 B4O 0.8597
295 64C 0.8597
296 JGB 0.8594
297 209 0.8593
298 94W 0.8588
299 G1P 0.8586
300 DQU 0.8584
301 4NO 0.8583
302 9FE 0.8583
303 62D 0.8581
304 PMP 0.8580
305 HHR 0.8580
306 NGA 0.8575
307 9ZE 0.8573
308 JF8 0.8572
309 M3F 0.8571
310 7MX 0.8568
311 GI3 0.8566
312 92O 0.8565
313 ONR 0.8563
314 0FK 0.8563
315 WSD 0.8562
316 D1G 0.8562
317 39O 0.8561
318 JWS 0.8556
319 3D8 0.8556
320 MS9 0.8552
321 CTE 0.8548
322 NOM 0.8545
323 LDC 0.8543
324 8HC 0.8542
325 K48 0.8540
326 5SB 0.8523
327 E7R 0.8521
328 MXD 0.8520
329 4AA 0.8507
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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