Receptor
PDB id Resolution Class Description Source Keywords
6DJG 1.88 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ503 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
GNJ A:702;
B:702;
 Valid;
Valid;
 none;
none;
 submit data
269.231 C10 H7 N O6 S c1cc2...
EDO A:701;
B:701;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
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: GNJ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 GNJ 1 1
2 GNV 0.6 0.622642
Similar Ligands (3D)
Ligand no: 1; Ligand: GNJ; Similar ligands found: 293
No: Ligand Similarity coefficient
1 JTA 0.9716
2 GNY 0.9630
3 WUB 0.9310
4 GNM 0.9236
5 67X 0.9191
6 49P 0.9187
7 30G 0.9145
8 VKE 0.9134
9 JP2 0.9130
10 IQZ 0.9127
11 1X8 0.9109
12 MS0 0.9104
13 CKA 0.9100
14 LF5 0.9098
15 U7E 0.9096
16 2JK 0.9094
17 KM2 0.9088
18 P9I 0.9084
19 CNI 0.9077
20 OCZ 0.9074
21 YE7 0.9064
22 IQ5 0.9063
23 TCR 0.9059
24 5F8 0.9057
25 EV2 0.9052
26 549 0.9040
27 KW8 0.9037
28 HNA 0.9027
29 F40 0.9022
30 982 0.9020
31 LP8 0.9020
32 9TF 0.9019
33 774 0.9015
34 7I2 0.9009
35 NRA 0.9003
36 XM5 0.9002
37 MNX 0.9001
38 5TZ 0.8994
39 6TJ 0.8993
40 FUJ 0.8985
41 DRG 0.8985
42 344 0.8980
43 DK1 0.8978
44 KLV 0.8978
45 2GQ 0.8976
46 DNQ 0.8975
47 9CE 0.8972
48 II4 0.8966
49 VM1 0.8965
50 EWG 0.8965
51 NAG 0.8961
52 0LO 0.8958
53 THA 0.8955
54 LL1 0.8954
55 B21 0.8950
56 5GT 0.8950
57 27M 0.8947
58 TXW 0.8945
59 9AP 0.8945
60 8G6 0.8943
61 LDR 0.8943
62 BA5 0.8940
63 F2W 0.8935
64 7FF 0.8933
65 2J2 0.8932
66 BGU 0.8931
67 ZSP 0.8927
68 5V7 0.8925
69 5FL 0.8925
70 537 0.8919
71 GDL 0.8918
72 JRO 0.8916
73 DX7 0.8912
74 DXK 0.8911
75 L3L 0.8910
76 761 0.8904
77 QR2 0.8904
78 0XT 0.8904
79 1V3 0.8899
80 RVE 0.8895
81 E1K 0.8895
82 HRM 0.8894
83 5WT 0.8893
84 F95 0.8889
85 AH3 0.8887
86 3Y7 0.8887
87 2LW 0.8885
88 3J8 0.8883
89 I7B 0.8882
90 0SX 0.8880
91 1FL 0.8879
92 S60 0.8877
93 C8O 0.8877
94 1AJ 0.8870
95 54X 0.8865
96 HBO 0.8864
97 ALR 0.8864
98 H4B 0.8858
99 PRL 0.8857
100 YZ9 0.8856
101 EMO 0.8856
102 Q8G 0.8850
103 5NS 0.8849
104 BIK 0.8844
105 BPU 0.8843
106 64C 0.8842
107 OAI 0.8839
108 LZ2 0.8838
109 LEL 0.8835
110 DX1 0.8832
111 DPT 0.8831
112 BIO 0.8829
113 AA 0.8828
114 P4L 0.8827
115 1YL 0.8826
116 CX6 0.8823
117 S62 0.8823
118 CUE 0.8822
119 AMR 0.8821
120 5F5 0.8820
121 ANC 0.8819
122 AO6 0.8818
123 J1K 0.8818
124 JG8 0.8818
125 64E 0.8816
126 ANF 0.8813
127 4AU 0.8812
128 5VJ 0.8810
129 78Y 0.8810
130 D87 0.8809
131 39Z 0.8808
132 2J1 0.8806
133 LFQ 0.8803
134 19E 0.8803
135 9UL 0.8801
136 V2Z 0.8800
137 6FB 0.8798
138 NDG 0.8798
139 YE6 0.8796
140 5P3 0.8795
141 6ZW 0.8794
142 4RV 0.8793
143 TXQ 0.8791
144 HKK 0.8789
145 L07 0.8787
146 V1T 0.8787
147 CZ0 0.8782
148 TIY 0.8779
149 X0W 0.8777
150 FCD 0.8775
151 IL5 0.8773
152 HC8 0.8772
153 582 0.8772
154 5NN 0.8771
155 6QF 0.8768
156 68A 0.8767
157 MUR 0.8766
158 ZME 0.8765
159 EV3 0.8761
160 5SB 0.8758
161 FQX 0.8758
162 LJW 0.8756
163 H05 0.8756
164 AZN 0.8751
165 LWS 0.8748
166 9KZ 0.8747
167 NOM 0.8746
168 CLI 0.8744
169 692 0.8743
170 4FF 0.8742
171 TK4 0.8740
172 K44 0.8739
173 X11 0.8738
174 1EL 0.8737
175 272 0.8735
176 SER DNF 0.8732
177 1KP 0.8730
178 P83 0.8727
179 DNF SER 0.8722
180 ET0 0.8722
181 A73 0.8721
182 HBI 0.8721
183 JWS 0.8721
184 1V4 0.8721
185 LUM 0.8719
186 6X9 0.8714
187 OTA 0.8709
188 5TY 0.8709
189 1V1 0.8704
190 C09 0.8695
191 2WU 0.8695
192 CKU 0.8694
193 D80 0.8690
194 PTS 0.8690
195 20D 0.8687
196 WS7 0.8686
197 AXX 0.8685
198 RKV 0.8685
199 HA6 0.8684
200 FLV 0.8684
201 AMU 0.8682
202 18E 0.8681
203 QMS 0.8678
204 S98 0.8676
205 JF8 0.8675
206 AH9 0.8675
207 2D2 0.8675
208 CSN 0.8674
209 8NX 0.8674
210 78P 0.8671
211 T28 0.8669
212 HH6 0.8667
213 EY2 0.8667
214 4MU 0.8666
215 AJ1 0.8665
216 0FR 0.8661
217 9RM 0.8660
218 B98 0.8660
219 ITE 0.8659
220 A5H 0.8658
221 NLA 0.8657
222 UN9 0.8656
223 9XZ 0.8655
224 XEZ 0.8654
225 SU9 0.8653
226 2PW 0.8653
227 WLH 0.8651
228 K25 0.8650
229 3GX 0.8647
230 DFL 0.8645
231 PEY 0.8642
232 Q8D 0.8641
233 VUP 0.8641
234 4G2 0.8639
235 ADL 0.8637
236 1QV 0.8637
237 HRD 0.8635
238 NKI 0.8635
239 BPY 0.8633
240 D1G 0.8632
241 IDZ 0.8629
242 7B3 0.8628
243 4TU 0.8626
244 2QU 0.8625
245 R6T 0.8624
246 226 0.8622
247 QVK 0.8621
248 GHM 0.8620
249 3R4 0.8619
250 K48 0.8615
251 22T 0.8615
252 EST 0.8613
253 5PX 0.8612
254 Z21 0.8612
255 RHN 0.8610
256 OPA 0.8607
257 6JO 0.8603
258 SRO 0.8601
259 DT7 0.8601
260 DX2 0.8601
261 GNR 0.8599
262 M3F 0.8599
263 25F 0.8597
264 55D 0.8595
265 J38 0.8593
266 L1T 0.8593
267 1DR 0.8591
268 DBF 0.8590
269 PLP 0.8588
270 5E5 0.8588
271 AVR 0.8586
272 N0Z 0.8586
273 7M5 0.8585
274 3QV 0.8585
275 N2M 0.8584
276 KYA 0.8583
277 34L 0.8580
278 9OF 0.8577
279 6DQ 0.8575
280 I6G 0.8575
281 IBM 0.8566
282 BBY 0.8565
283 XYS XYP 0.8565
284 AJY 0.8561
285 LIG 0.8559
286 AY4 0.8559
287 3SU 0.8546
288 N88 0.8545
289 MHK 0.8542
290 7M2 0.8529
291 4I8 0.8523
292 SZ5 0.8521
293 CC6 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
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