Receptor
PDB id Resolution Class Description Source Keywords
5kr7 1.9 Å EC: 1.14.11.- KDM4C BOUND TO PYRAZOLO-PYRIMIDINE SCAFFOLD HOMO SAPIENS INHIBITOR HISTONE LYSINE DEMETHYLASE OXIDOREDUCTASE
Ref.: IDENTIFICATION OF POTENT, SELECTIVE KDM5 INHIBITORS BIOORG.MED.CHEM.LETT. V. 26 4350 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:402;
B:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
6X9 A:403;
B:403;
Valid;
Valid;
none;
none;
ic50 = 2.88 uM
216.239 C11 H12 N4 O CCC1=...
CL B:404;
A:404;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
FE2 B:401;
A:401;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KR7 1.9 Å EC: 1.14.11.- KDM4C BOUND TO PYRAZOLO-PYRIMIDINE SCAFFOLD HOMO SAPIENS INHIBITOR HISTONE LYSINE DEMETHYLASE OXIDOREDUCTASE
Ref.: IDENTIFICATION OF POTENT, SELECTIVE KDM5 INHIBITORS BIOORG.MED.CHEM.LETT. V. 26 4350 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 families.
1 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
2 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (49)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
40 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
41 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
42 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
44 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
45 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
46 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
47 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
48 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
49 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6H4T Ki = 0.004 uM FOW C25 H26 N6 O c1ccc2c(c1....
2 5A7P - 6Z1 C17 H13 N3 O5 Cc1cc(no1)....
3 5ANQ ic50 = 3.98 uM 5YQ C16 H13 N5 O2 c1cc(cnc1)....
4 6H4Q ic50 = 2.06 uM FO2 C16 H18 N6 O CN1CCC(CC1....
5 2OQ6 - OGA C4 H5 N O5 C(C(=O)O)N....
6 2OX0 - OGA C4 H5 N O5 C(C(=O)O)N....
7 6H4S Ki = 0.002 uM FQE C27 H33 N7 O CN(C)CCc1c....
8 5F3G ic50 = 0.126 uM 5UL C24 H25 Cl N6 O c1cc(ccc1C....
9 5A7Q - KCH C12 H10 N2 O3 c1cc(c(cc1....
10 6H4P Ki = 0.003 uM FQ5 C23 H23 Cl N6 O c1cc(cc(c1....
11 5A7N - VAO C13 H8 N2 O3 c1cc(c(cc1....
12 5F3E ic50 = 0.138 uM 5UO C23 H23 Cl N6 O c1cc(ccc1C....
13 2GP5 - AKG C5 H6 O5 C(CC(=O)O)....
14 6H4V ic50 = 0.613 uM FQN C20 H24 N6 O c1cnc(c2c1....
15 6H4O ic50 = 0.128 uM FQH C24 H23 F3 N6 O c1cc(cc(c1....
16 2OT7 - OGA C4 H5 N O5 C(C(=O)O)N....
17 6H4U - FO2 C16 H18 N6 O CN1CCC(CC1....
18 5A7S - S2X C14 H12 N2 O4 CC(=O)Nc1c....
19 6H4R Ki = 0.004 nM FQB C27 H33 N7 O CN(C)CCc1c....
20 4AI9 - DZA C6 H12 N2 O3 CN(C)NC(=O....
21 3U4S Ki = 114 nM ALA ARG M3L SER CYS GLY GLY LYS 08P n/a n/a
22 3PDQ ic50 = 0.18 uM KC6 C14 H14 N4 O3 c1cnc(cc1C....
23 5F3C ic50 = 0.9 uM 5U8 C20 H19 F N6 O CN(CCc1cnn....
24 5F32 ic50 = 11.5 uM 5V7 C10 H7 N5 O S c1cnc(c2c1....
25 4URA ic50 = 0.00000316 uM LEL C8 H6 N4 O2 c1cnc(cc1C....
26 5F2S ic50 = 0.2 uM 5TZ C9 H7 N3 O2 S c1cnc(cc1C....
27 2YBK ic50 = 24 uM 2HG C5 H8 O5 C(CC(=O)O)....
28 5TVR - AKG C5 H6 O5 C(CC(=O)O)....
29 5A80 - 9CJ C21 H18 N2 O5 COc1cccc(c....
30 6H4Y ic50 = 0.077 uM FO8 C29 H35 N7 O2 c1cc(ccc1C....
31 5A7O - 7WH C15 H14 N2 O5 COCC(=O)Nc....
32 6CG1 - QC1 C13 H11 F N2 O2 c1cc(ccc1C....
33 5F37 ic50 = 1.7 uM N5J C7 H5 N3 O c1cncc2c1C....
34 6H4X ic50 = 0.131 uM FNQ C28 H27 N7 O c1cc(cnc1)....
35 6CG2 - QC2 C15 H11 N3 O3 c1cc(cc(c1....
36 2OQ7 - OGA C4 H5 N O5 C(C(=O)O)N....
37 5FPV - MMK C15 H22 N4 O3 CCN(/C=C/N....
38 5F3I ic50 = 0.08 uM 5UJ C23 H22 Cl2 N6 O c1cnc(c2c1....
39 3OPT - AKG C5 H6 O5 C(CC(=O)O)....
40 5KR7 ic50 = 2.88 uM 6X9 C11 H12 N4 O CCC1=C(Nc2....
41 4XDO ic50 = 84 uM OGA C4 H5 N O5 C(C(=O)O)N....
42 5FP4 ic50 = 0.251 uM YC8 C16 H16 N2 O3 c1ccc(cc1)....
43 5FP7 - YC8 C16 H16 N2 O3 c1ccc(cc1)....
44 5F5C - 5V3 C15 H14 N4 O c1ccc(cc1)....
45 5FP8 - AUY C12 H12 N2 O2 S Cc1cc(sc1)....
46 5F5A - 5V0 C12 H12 N2 O3 c1cc(oc1)C....
47 5FP9 ic50 = 1.585 uM 4SV C6 H6 N2 O2 c1cncc(c1C....
48 5FPA - N5J C7 H5 N3 O c1cncc2c1C....
49 5FPB - HA6 C10 H7 N5 O2 c1cncc2c1C....
50 4HON - THR ALA ARG M3L SER THR GLY GLY LYS ALA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6X9; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6X9 1 1
2 4VS 0.483333 0.909091
Similar Ligands (3D)
Ligand no: 1; Ligand: 6X9; Similar ligands found: 346
No: Ligand Similarity coefficient
1 6E8 0.9490
2 1KP 0.9272
3 AJY 0.9270
4 39O 0.9267
5 TOF 0.9160
6 0XT 0.9144
7 30G 0.9127
8 64C 0.9106
9 AH9 0.9098
10 GF4 0.9092
11 I6G 0.9082
12 PH2 0.9072
13 UFO 0.9072
14 28N 0.9071
15 GNY 0.9064
16 N0Z 0.9061
17 GNM 0.9053
18 TIY 0.9051
19 HBO 0.9048
20 E7S 0.9046
21 HHR 0.9042
22 JU2 0.9025
23 CFF 0.9024
24 CLZ 0.9022
25 GNV 0.9009
26 1QP 0.9003
27 8W9 0.9002
28 AJV 0.8998
29 NAG 0.8993
30 2FQ 0.8982
31 G12 0.8982
32 V1T 0.8975
33 3J8 0.8970
34 N8Y 0.8969
35 7B3 0.8965
36 7MX 0.8965
37 PQ0 0.8963
38 3QV 0.8960
39 BDP 0.8957
40 HQD 0.8957
41 CCV 0.8956
42 KJ5 0.8953
43 K44 0.8950
44 X11 0.8948
45 GSY 0.8943
46 15E 0.8941
47 5QY 0.8941
48 8WO 0.8936
49 MUA 0.8933
50 JP2 0.8926
51 DX3 0.8925
52 JTA 0.8924
53 F2W 0.8923
54 JY4 0.8921
55 FLV 0.8919
56 HHS 0.8915
57 JG8 0.8912
58 X0W 0.8912
59 6BL 0.8912
60 0N7 0.8911
61 VXX 0.8910
62 BZJ 0.8909
63 LOG 0.8900
64 XM5 0.8896
65 6QF 0.8889
66 3N1 0.8884
67 DPT 0.8883
68 K6X 0.8880
69 BGU 0.8880
70 PHH 0.8878
71 K68 0.8877
72 64E 0.8874
73 2LY 0.8870
74 AZ9 0.8866
75 2AK 0.8864
76 RH1 0.8862
77 C9E 0.8860
78 C2Y 0.8858
79 HKD 0.8857
80 92P 0.8856
81 L1Q 0.8854
82 FDR 0.8850
83 ANC 0.8845
84 HRM 0.8844
85 DNA 0.8839
86 226 0.8838
87 9LI 0.8838
88 R9Y 0.8837
89 9R5 0.8836
90 0J5 0.8835
91 2K8 0.8834
92 CK2 0.8833
93 TTL 0.8832
94 68A 0.8832
95 EGR 0.8832
96 5TY 0.8828
97 BGC 0.8828
98 LT2 0.8825
99 B21 0.8825
100 PRF 0.8822
101 GJP 0.8821
102 5RO 0.8820
103 AH6 0.8815
104 0FK 0.8812
105 E1K 0.8810
106 H70 0.8808
107 3PF 0.8807
108 SRO 0.8805
109 SKM 0.8802
110 H4B 0.8802
111 3Z8 0.8801
112 2HQ 0.8799
113 ROI 0.8798
114 27B 0.8798
115 0FO 0.8795
116 THA 0.8791
117 0P6 0.8789
118 WSD 0.8788
119 ZYR 0.8787
120 APZ 0.8785
121 0FN 0.8784
122 HBI 0.8783
123 GDE 0.8783
124 KW8 0.8782
125 1A7 0.8782
126 WS6 0.8782
127 CNI 0.8781
128 8MO 0.8780
129 CB1 0.8780
130 LDR 0.8778
131 X8D 0.8778
132 86J 0.8775
133 BA5 0.8774
134 J6W 0.8772
135 TWO 0.8770
136 6ZW 0.8769
137 IQ5 0.8768
138 B62 0.8767
139 PEY 0.8766
140 D48 0.8765
141 MS9 0.8764
142 44V 0.8762
143 DX1 0.8761
144 NDG 0.8760
145 AH3 0.8760
146 9AP 0.8758
147 KUF 0.8758
148 DQU 0.8757
149 LDC 0.8755
150 AMR 0.8753
151 2J1 0.8753
152 WUB 0.8753
153 EAE 0.8751
154 537 0.8751
155 SYV 0.8750
156 8HC 0.8749
157 J5I 0.8748
158 HA5 0.8748
159 8S0 0.8747
160 9FL 0.8747
161 EVA 0.8746
162 EN1 0.8742
163 H4E 0.8740
164 G3E 0.8738
165 BIK 0.8738
166 6FB 0.8737
167 1HN 0.8736
168 B60 0.8736
169 G3F 0.8736
170 GLC 0.8731
171 15N 0.8731
172 4RU 0.8728
173 7WR 0.8728
174 0JD 0.8727
175 SE2 0.8727
176 CWS 0.8727
177 GTR 0.8726
178 A29 0.8725
179 4JQ 0.8724
180 BSP 0.8723
181 E7R 0.8721
182 JYB 0.8721
183 H5B 0.8720
184 TXW 0.8720
185 HNT 0.8719
186 DPZ 0.8719
187 JXN 0.8718
188 IV2 0.8718
189 37T 0.8716
190 ESI 0.8716
191 0F9 0.8715
192 344 0.8715
193 MAQ 0.8715
194 GNJ 0.8714
195 GCS 0.8714
196 9UL 0.8714
197 XDE 0.8713
198 FQX 0.8712
199 2J2 0.8712
200 BPU 0.8712
201 8CM 0.8710
202 4KL 0.8709
203 6RQ 0.8709
204 5AD 0.8708
205 X0U 0.8708
206 SNG 0.8705
207 ANF 0.8704
208 6ME 0.8698
209 2JK 0.8697
210 DRG 0.8694
211 GDL 0.8694
212 JXZ 0.8693
213 AA 0.8693
214 TT4 0.8693
215 RZH 0.8688
216 R8V 0.8688
217 QX4 0.8688
218 9FE 0.8685
219 BIO 0.8684
220 THM 0.8683
221 LI6 0.8680
222 GXY 0.8679
223 44W 0.8678
224 CH9 0.8676
225 AN3 0.8676
226 BPY 0.8675
227 XHP 0.8675
228 KGK 0.8675
229 3IT 0.8674
230 QSH 0.8670
231 F31 0.8670
232 1IT 0.8668
233 4AA 0.8667
234 4NC 0.8666
235 KYA 0.8663
236 L99 0.8663
237 5XL 0.8661
238 FGZ 0.8661
239 9KT 0.8659
240 4Z4 0.8657
241 9MG 0.8655
242 9KZ 0.8652
243 ALR 0.8652
244 Q7A 0.8652
245 KJU 0.8650
246 EV3 0.8650
247 ST1 0.8649
248 2O6 0.8648
249 7MK 0.8647
250 6KT 0.8646
251 P9P 0.8646
252 8NB 0.8642
253 E1T 0.8641
254 B56 0.8640
255 9CA 0.8638
256 209 0.8637
257 OTW 0.8636
258 SYR 0.8635
259 JF2 0.8633
260 GAL 0.8630
261 5V7 0.8630
262 5GV 0.8630
263 ARP 0.8627
264 PQK 0.8626
265 DHK 0.8625
266 MVN 0.8623
267 4ME 0.8622
268 4AN 0.8622
269 DHB 0.8618
270 LNR 0.8617
271 94W 0.8616
272 5GU 0.8615
273 5NS 0.8615
274 4TU 0.8614
275 ETV 0.8611
276 APS 0.8610
277 H33 0.8610
278 S60 0.8610
279 4MU 0.8610
280 MRW 0.8609
281 II4 0.8608
282 L7T 0.8608
283 VK3 0.8607
284 428 0.8607
285 JRO 0.8607
286 N2I 0.8606
287 7W1 0.8606
288 5QX 0.8606
289 774 0.8604
290 93K 0.8604
291 M5H 0.8604
292 8NX 0.8603
293 12Q 0.8601
294 7I2 0.8601
295 PXL 0.8600
296 K97 0.8600
297 XQK 0.8598
298 2KA 0.8597
299 KJH 0.8597
300 DUR 0.8596
301 KJY 0.8596
302 CHB 0.8596
303 5VL 0.8595
304 KT7 0.8593
305 9TW 0.8591
306 MQN 0.8590
307 DT9 0.8585
308 3R4 0.8585
309 BEA 0.8583
310 DIN 0.8582
311 DCZ 0.8581
312 B5D 0.8581
313 CKA 0.8580
314 JLZ 0.8580
315 4VY 0.8580
316 TIA 0.8578
317 CWJ 0.8578
318 ZME 0.8574
319 8WT 0.8573
320 HQT 0.8573
321 9ZE 0.8571
322 MXD 0.8570
323 4YO 0.8570
324 2D3 0.8569
325 0HO 0.8565
326 2HO 0.8565
327 S8A 0.8564
328 MYJ 0.8561
329 B0K 0.8558
330 DNF 0.8558
331 K37 0.8556
332 SKA 0.8554
333 RDT 0.8553
334 L22 0.8552
335 N2M 0.8552
336 XX2 0.8549
337 CTS 0.8549
338 DNC 0.8544
339 D07 0.8541
340 DDU 0.8538
341 0HN 0.8537
342 INO 0.8530
343 TCR 0.8530
344 I7B 0.8525
345 A7W 0.8523
346 0TU 0.8510
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KR7; Ligand: 6X9; 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: 5kr7.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KR7; Ligand: 6X9; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 5kr7.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6IP0 AKG 42.2343
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