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Receptor
PDB id Resolution Class Description Source Keywords
5EQY 2.5 Å EC: 2.7.1.32 CRYSTAL STRUCTURE OF CHOLINE KINASE ALPHA-1 BOUND BY 5-[(4-M DIAZEPAN-1-YL)METHYL]-2-[4-[(4-METHYL-1,4-DIAZEPAN-1-YL) M ETHYL]PHENYL]BENZENECARBONITRILE (COMPOUND 65) HOMO SAPIENS KINASE INHIBITOR DRUG TARGET TRANSFERASE-TRANSFERASE INHICOMPLEX
Ref.: NOVEL SMALL MOLECULE INHIBITORS OF CHOLINE KINASE I BY FRAGMENT-BASED DRUG DISCOVERY. J.MED.CHEM. V. 59 671 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5RA A:501;
B:501;
Valid;
Valid;
none;
none;
ic50 = 0.07 uM
431.616 C27 H37 N5 CN1CC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EQY 2.5 Å EC: 2.7.1.32 CRYSTAL STRUCTURE OF CHOLINE KINASE ALPHA-1 BOUND BY 5-[(4-M DIAZEPAN-1-YL)METHYL]-2-[4-[(4-METHYL-1,4-DIAZEPAN-1-YL) M ETHYL]PHENYL]BENZENECARBONITRILE (COMPOUND 65) HOMO SAPIENS KINASE INHIBITOR DRUG TARGET TRANSFERASE-TRANSFERASE INHICOMPLEX
Ref.: NOVEL SMALL MOLECULE INHIBITORS OF CHOLINE KINASE I BY FRAGMENT-BASED DRUG DISCOVERY. J.MED.CHEM. V. 59 671 2016
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3ZM9 - QMQ C30 H34 N7 CN(C)c1cc[....
2 5EQY ic50 = 0.07 uM 5RA C27 H37 N5 CN1CCCN(CC....
3 5FUT Ki = 4.1 uM PQ7 C34 H42 N4 CN(C)c1cc[....
4 4CG9 - GQG C20 H21 N2 CN(C)c1cc[....
5 4CG8 ic50 = 1.2 uM G8S C37 H41 Cl N4 CN(C)c1cc[....
6 5AFV Kd = 2.6 uM JH5 C16 H17 N4 c1ccc(cc1)....
7 5EQE ic50 = 87 uM 5R8 C14 H23 N3 CN1CCCN(CC....
8 5FTG Kd = 0.7 uM NBR C30 H36 N4 O2 CN(C)C1=CC....
9 2CKQ - PC C5 H15 N O4 P C[N+](C)(C....
10 5W6O ic50 = 520 nM 9X1 C46 H38 Cl2 N4 CN(c1ccc(c....
11 5EQP ic50 = 3.9 uM 5R9 C16 H21 N3 CN1CCCN(CC....
12 4BR3 Kd = 1.9 uM U85 C26 H26 N7 CN(C)c1cc[....
13 4CGA - QLW C22 H25 N2 CN(C)c1cc[....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3ZM9 - QMQ C30 H34 N7 CN(C)c1cc[....
2 5EQY ic50 = 0.07 uM 5RA C27 H37 N5 CN1CCCN(CC....
3 5FUT Ki = 4.1 uM PQ7 C34 H42 N4 CN(C)c1cc[....
4 4CG9 - GQG C20 H21 N2 CN(C)c1cc[....
5 4CG8 ic50 = 1.2 uM G8S C37 H41 Cl N4 CN(C)c1cc[....
6 5AFV Kd = 2.6 uM JH5 C16 H17 N4 c1ccc(cc1)....
7 5EQE ic50 = 87 uM 5R8 C14 H23 N3 CN1CCCN(CC....
8 5FTG Kd = 0.7 uM NBR C30 H36 N4 O2 CN(C)C1=CC....
9 2CKQ - PC C5 H15 N O4 P C[N+](C)(C....
10 5W6O ic50 = 520 nM 9X1 C46 H38 Cl2 N4 CN(c1ccc(c....
11 5EQP ic50 = 3.9 uM 5R9 C16 H21 N3 CN1CCCN(CC....
12 4BR3 Kd = 1.9 uM U85 C26 H26 N7 CN(C)c1cc[....
13 4CGA - QLW C22 H25 N2 CN(C)c1cc[....
14 4DA5 Ki = 0.36 uM 0H7 C16 H17 Cl2 N O S2 c1cc(sc1C(....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3ZM9 - QMQ C30 H34 N7 CN(C)c1cc[....
2 5EQY ic50 = 0.07 uM 5RA C27 H37 N5 CN1CCCN(CC....
3 5FUT Ki = 4.1 uM PQ7 C34 H42 N4 CN(C)c1cc[....
4 4CG9 - GQG C20 H21 N2 CN(C)c1cc[....
5 4CG8 ic50 = 1.2 uM G8S C37 H41 Cl N4 CN(C)c1cc[....
6 5AFV Kd = 2.6 uM JH5 C16 H17 N4 c1ccc(cc1)....
7 5EQE ic50 = 87 uM 5R8 C14 H23 N3 CN1CCCN(CC....
8 5FTG Kd = 0.7 uM NBR C30 H36 N4 O2 CN(C)C1=CC....
9 2CKQ - PC C5 H15 N O4 P C[N+](C)(C....
10 5W6O ic50 = 520 nM 9X1 C46 H38 Cl2 N4 CN(c1ccc(c....
11 5EQP ic50 = 3.9 uM 5R9 C16 H21 N3 CN1CCCN(CC....
12 4BR3 Kd = 1.9 uM U85 C26 H26 N7 CN(C)c1cc[....
13 4CGA - QLW C22 H25 N2 CN(C)c1cc[....
14 4DA5 Ki = 0.36 uM 0H7 C16 H17 Cl2 N O S2 c1cc(sc1C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5RA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 5RA 1 1
2 5R8 0.507937 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EQY; Ligand: 5RA; Similar sites found with APoc: 443
This union binding pocket(no: 1) in the query (biounit: 5eqy.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
1 4CSD MFU None
2 6F7X MFU None
3 4RJD TFP None
4 5C03 AGS 1.16959
5 2GU8 796 1.18694
6 5HCY 60D 1.20846
7 4WOV 3SM 1.26183
8 5EO8 TFU 1.28617
9 3Q60 ATP 1.34771
10 5DMZ ADP 1.36986
11 3PN1 IVH 1.57233
12 4U98 ACP 1.74564
13 5OES ADP 1.74564
14 3K5I ADP 1.74564
15 4WB7 ATP 1.74564
16 2PVF ACP 1.79641
17 1Q8Y ADE 1.87668
18 1Q8Y ADP 1.87668
19 3ZGJ RMN 1.88679
20 5BVE 4VG 1.93906
21 5JFS 6K0 1.94805
22 2B9J ADP 1.99501
23 3V8S 0HD 1.99501
24 2B9I ADP 1.99501
25 2B9F ADP 1.99501
26 2B9H ADP 1.99501
27 3PTG 932 1.99501
28 3TTI KBI 1.99501
29 3E7O 35F 1.99501
30 5JM8 ATP 1.99501
31 4WB6 ATP 2
32 1RE8 BD2 2
33 3PLS ANP 2.01342
34 3WVR AMP 2.01342
35 4DC2 ADE 2.0202
36 2V7O DRN 2.08333
37 3KRL KRL 2.08955
38 4NFE BEN 2.1097
39 5KO1 6UY 2.12014
40 6GQM F8H 2.13415
41 1IA9 ANP 2.14286
42 4K33 ACP 2.15385
43 4UXL 5P8 2.17391
44 5FBN 5WF 2.21402
45 3SXS PP2 2.23881
46 1Y57 MPZ 2.24439
47 2H8H H8H 2.24439
48 2RIO ADP 2.24439
49 5LI1 ANP 2.25989
50 4AUA 4AU 2.28013
51 5LI9 ACP 2.28571
52 5C1P ADP 2.28758
53 1OBD ATP 2.28758
54 5C1P DAL DAL 2.28758
55 6C0T EE4 2.30548
56 6GIN IR2 2.32558
57 4G31 0WH 2.34114
58 4QTB 38Z 2.36842
59 6BXI ANP 2.4024
60 1S68 AMP 2.40964
61 3UIM ANP 2.45399
62 1Z2P I3S 2.46914
63 1Z2P ACP 2.46914
64 4UX9 ANP 2.47253
65 5UIU 8CG 2.47678
66 4H3P ANP 2.48619
67 4H3Q ANP 2.48619
68 4CYI ATP 2.49377
69 5IM3 DTP 2.49377
70 6A1G 9OL 2.5
71 5TA6 79D 2.51397
72 1GSA ADP 2.53165
73 4D52 GXL 2.53968
74 4D52 GIV 2.53968
75 5DH3 5BS 2.53968
76 1DL2 NAG NAG BMA 2.54403
77 3TXO 07U 2.54958
78 4IX4 ADP 2.57143
79 1U5R ATP 2.58621
80 4OUJ LBT 2.60586
81 3HMO STU 2.63158
82 4OTH DRN 2.6393
83 4E93 GUI 2.65252
84 4I94 ANP 2.66667
85 3PAK MAN 2.7027
86 6F3G CJN 2.71186
87 5W4W 9WG 2.71903
88 4KBA 1QM 2.71903
89 4XV1 904 2.73973
90 4UWH JXM 2.74314
91 3ETH ATP 2.74314
92 6EZ6 C5Z 2.74314
93 2X3J ATP 2.74314
94 5DXT 5H5 2.74314
95 5AE9 OKO 2.74314
96 1U59 STU 2.78746
97 4CC6 L5Y 2.83019
98 1BYG STU 2.8777
99 4CQE CQE 2.8777
100 2OFV 242 2.88809
101 4EWH T77 2.90909
102 3ORQ ADP 2.91777
103 5ZCT ANP 2.94118
104 4LRJ ANP 2.95858
105 5WO4 B7V 2.98013
106 5IGI GMP 2.99003
107 5IGI ZIT 2.99003
108 2QK4 ATP 2.99252
109 4AT3 LTI 3.01003
110 1W2D ADP 3.01887
111 1W2D 4IP 3.01887
112 4G17 0VN 3.0303
113 5I35 ANP 3.05344
114 5KBE IPH 3.05677
115 5USZ SKE 3.11419
116 2Z7R STU 3.11526
117 1T36 ADP 3.14136
118 3G5D 1N1 3.14685
119 2WU6 DKI 3.14961
120 5G1X ADP 3.15789
121 5QIN J2V 3.16456
122 5GLT BGC GAL NAG GAL 3.16901
123 4BCS BTN 3.2
124 4A4X JUP 3.22581
125 4O4F ATP 3.22581
126 4O4F IHP 3.22581
127 4UAL 3FV 3.2419
128 4Y93 746 3.2419
129 1PK8 ATP 3.2419
130 3O01 DXC 3.24675
131 5HES 032 3.25733
132 1IOW ADP 3.26797
133 4GYI ADP 3.27456
134 3SLS ANP 3.28947
135 1KJ8 ATP 3.32481
136 1K3A ACP 3.34448
137 3LXK MI1 3.36391
138 4DFU QUE 3.41615
139 5VC5 96M 3.46021
140 6ES0 BW8 3.47003
141 3VOT ADP 3.49127
142 4O1P ANP 3.49127
143 4PNI KQQ 3.49127
144 4L9I 8PR 3.49127
145 2VQD AP2 3.49127
146 3C1X CKK 3.49127
147 5WNL STU 3.50877
148 4M69 ANP 3.53357
149 5NKB 8ZT 3.59477
150 4CSV STI 3.63636
151 3H9R TAK 3.66972
152 3AKK ADP 3.69231
153 5FI4 5XV 3.71517
154 1DTL BEP 3.72671
155 4AZW ATP 3.74065
156 4OAV ACP 3.74065
157 3UDZ ADP 3.74065
158 6FL8 ADP 3.74065
159 6FL8 TIY 3.74065
160 4KS7 X4Z 3.76712
161 2QX0 PH2 3.77358
162 3MVH WFE 3.80117
163 3V4S ATP 3.87597
164 3V4S ADP 3.87597
165 4I6H 1C8 3.8961
166 3TDV GDP 3.92157
167 4OUC 5ID 3.92157
168 6G34 5ID 3.92157
169 5GZ9 ANP 3.93443
170 4YMJ 4EJ 3.94737
171 2WEL K88 3.97554
172 5CKW ANP 3.99003
173 5DZT AMP 3.99003
174 2A19 ANP 4
175 3HAV ATP 4.01338
176 2Q7D ANP 4.04624
177 4IZY 1J2 4.06504
178 1CM8 ANP 4.08719
179 6BFN DL1 4.09357
180 5XVG 8FX 4.09556
181 2IF8 ADP 4.13223
182 2VZ6 FEF 4.15335
183 5LVP ATP 4.18006
184 3ORK AGS 4.18006
185 1AUX AGS 4.18006
186 3RWP ABQ 4.18006
187 4BFM ANP 4.19162
188 4BHN BH9 4.19162
189 4YZC STU 4.19753
190 4OH4 ANP 4.2042
191 4IDT T28 4.21348
192 5LPZ ADP 4.21687
193 4ONA UW1 4.2394
194 1EHI ADP 4.24403
195 5Y86 HRM 4.2517
196 3VPD ANP 4.27046
197 6GZD LCI 4.27807
198 2VN9 GVD 4.31894
199 3X01 AMP 4.3257
200 4LH7 1X8 4.33437
201 5EOB 5QQ 4.38871
202 2OVD DAO 4.3956
203 3E8N VRA 4.39883
204 3E8N ATP 4.39883
205 6GWR FEW 4.44444
206 3FHR P4O 4.46429
207 4IJP 1EH 4.46927
208 3TII ANP 4.47368
209 4NST AF3 4.47761
210 5EFQ ADP 4.47761
211 4NST ADP 4.47761
212 1M0W ANP 4.48878
213 3IGO ANP 4.48878
214 4MV1 ADP 4.48878
215 4PU5 ANP 4.48878
216 4QMN DB8 4.51613
217 4Y85 499 4.51807
218 4YZN 4K5 4.52962
219 5AWM ANP 4.56853
220 5T8O 76Z 4.58453
221 1ZTH ADP 4.65116
222 1ZP9 ATP 4.65116
223 3GGF GVD 4.65116
224 6FYL 3NG 4.6832
225 3GNI ATP 4.69208
226 5LPB ADP 4.72973
227 3VHE 42Q 4.73538
228 4WTV ATP 4.73815
229 6C1S EFV 4.73815
230 5N87 N66 4.79233
231 4ASE AV9 4.81586
232 5EKO N17 4.85175
233 5X8I SQZ 4.91329
234 1XJD STU 4.92754
235 1TQP ATP 4.96454
236 2IO8 ADP 4.98753
237 6G33 5ID 5.01475
238 6FYV 3NG 5.04451
239 3AQV TAK 5.07246
240 5ODY 9SK 5.07246
241 3FC2 IBI 5.07463
242 4FG8 ATP 5.07937
243 5U6C 7YS 5.07937
244 5JGA 6KC 5.07937
245 2X2M X2M 5.09554
246 5OMY 9YE 5.11509
247 1OFZ FUC 5.12821
248 2HZQ STR 5.17241
249 4RDL FUC GAL NDG FUC 5.19481
250 4XH0 ADP 5.23691
251 4U44 3D9 5.23691
252 5MW8 ATP 5.23691
253 4FL3 ANP 5.23691
254 2JLD AG1 5.23691
255 4P5Z Q7M 5.26316
256 4OCJ NDG 5.27704
257 2PUL ACP 5.28967
258 6CMJ F6J 5.29595
259 1ULE GLA GAL NAG 5.33333
260 3LXN MI1 5.34591
261 3M2W L8I 5.35117
262 4AG8 AXI 5.37975
263 5DEY 59T 5.38721
264 3ZRM ZRM 5.39084
265 5LXT ACP 5.46875
266 5VLQ ANP 5.48628
267 1I7L ATP 5.50162
268 3KN5 ANP 5.53846
269 4OCV ANP 5.5409
270 3IDB ANP 5.59006
271 5C4L 4XR 5.60748
272 5C4L SIS 5.60748
273 4GJ3 0XP 5.62914
274 3AJH BL3 5.64516
275 2ZV2 609 5.7047
276 3F7Z 34O 5.71429
277 4U0I 0LI 5.71429
278 5OKT 9XK 5.73248
279 5YK1 ANP 5.73566
280 5VZ0 ADP 5.73566
281 4XYM A12 5.73566
282 4XZ3 ACP 5.73566
283 4AU8 Z3R 5.74324
284 5DBX ANP 5.79268
285 3RE4 TO1 5.81395
286 2YAB AMP 5.81717
287 4E1Z 0MX 5.84192
288 2HY0 306 5.90062
289 2GQR ADP 5.90717
290 2GQS ADP 5.90717
291 4WNP 3RJ 5.92335
292 6AC9 ANP 5.94595
293 3DLS ADP 5.97015
294 5L8L ADP 5.98291
295 5A6N U7E 6.00707
296 1JPA ANP 6.08974
297 5UR1 YY9 6.10932
298 4ZGP ADP 6.14334
299 5AX9 4KT 6.16883
300 3PP0 03Q 6.21302
301 3GC8 B45 6.21622
302 5MJA 7O3 6.22951
303 3PVW QRX 6.23441
304 2BMB PMM 6.23441
305 6E1Q CFA 6.23441
306 2WEI VGG 6.27178
307 5CEO 50D 6.33333
308 2BPM 529 6.41509
309 4EKQ NPO 6.41711
310 2R5T ANP 6.43432
311 5UKL SIX 6.45161
312 2F2U M77 6.48379
313 4X7Q 3YR 6.48379
314 3DNT ATP 6.48379
315 2CFM AMP 6.48379
316 2HGS ADP 6.48379
317 5M06 ADP 6.52174
318 2Y6O 1N1 6.52921
319 3DAK ANP 6.55172
320 4USF 6UI 6.57895
321 1VYF OLA 6.66667
322 1OPK P16 6.66667
323 4CRL C1I 6.73317
324 2CSN CKI 6.73401
325 2WQN ADP 6.77419
326 3I0O ADP 6.78466
327 3EKK GS2 6.84039
328 1ZY5 ANP 6.93069
329 4FE2 ADP 7.05882
330 3GQI ACP 7.07965
331 3RK0 AMP 7.173
332 1IR3 ANP 7.18954
333 2R7K ACP 7.20222
334 2R7K AMZ 7.20222
335 3TPV ADE 7.23192
336 2AQX ATP 7.26644
337 1TZD ADP 7.27273
338 5EH0 5NW 7.36434
339 1PHK ATP 7.38255
340 5JZJ AN2 7.40741
341 2QCS ANP 7.56014
342 2F57 23D 7.57098
343 2YAK OSV 7.7193
344 2PYW ADP 7.73067
345 2YRX AMP 7.73067
346 2VPQ ANP 7.73067
347 4L3L 5FI 7.89474
348 5TDF ADP 8.02469
349 5K2M ADP 8.05861
350 3SAO NKN 8.125
351 6GUE FB8 8.20895
352 1VJY 460 8.25082
353 3C0G 3AM 8.26211
354 3RI1 3RH 8.30671
355 2BKK ADP 8.33333
356 1V0O INR 8.33333
357 3TM0 ANP 8.36502
358 3TM0 B31 8.36502
359 4BCQ TJF 8.39695
360 4BCM T7Z 8.39695
361 4CFU 2WC 8.39695
362 4BCN T9N 8.39695
363 4WNK 453 8.4788
364 5LMK 6ZK 8.52713
365 4JR7 GNP 8.55615
366 5VCV 1N1 8.68167
367 5OLK DTP 8.72818
368 3GC0 AMP 8.81459
369 4LO2 GAL BGC 8.84354
370 5IH9 6BF 8.95522
371 3HZT J60 8.97756
372 5IH1 GDP 8.97756
373 5IH1 6BQ 8.97756
374 2PVN P63 9.09091
375 3CY2 MB9 9.23567
376 2QLU ADE 9.23567
377 2XK9 XK9 9.31677
378 2Z77 HE7 9.35252
379 4EUU BX7 9.40439
380 4ZS4 ATP 9.44625
381 3VRY B43 9.47631
382 4CS9 AMP 9.52381
383 4NW6 2NS 9.59752
384 5ZTN CUR 9.72569
385 5MY8 RXZ 9.92167
386 5YW5 ADE 10.0559
387 3ALN ANP 10.0917
388 4LOO SB4 10.3448
389 5UPK ANP 10.4167
390 4F9C 0SX 10.4167
391 3OYW TDG 10.4478
392 3PDT ADP 10.5455
393 2J7T 274 10.596
394 5K21 6QF 10.6383
395 5DRB 5FJ 10.6529
396 6GU6 1QK 10.7143
397 5HQ0 LZ9 10.7143
398 6CQF F97 10.7744
399 3VPC ADP 10.9929
400 3VPB ADP 10.9929
401 6C7Y ADP 11.1111
402 6CGD AKN 11.1475
403 6CGD GNP 11.1475
404 3SRV S19 11.1913
405 4Y0X ADP 11.2
406 2PZI AXX 11.2219
407 2YW2 ATP 11.2219
408 1E4E ADP 11.3703
409 4Y24 TD2 11.6883
410 4WW7 AMP 11.7647
411 2GOO NDG 11.7647
412 5H9P TD2 12.0253
413 2P7Q GG6 12.0301
414 5HVJ ANP 12.0635
415 5ODT ADP 13.0435
416 5YF9 NIO 13.2743
417 5EYK 5U5 13.5593
418 3W0O ADP 13.7536
419 3W0O HY0 13.7536
420 2HK5 1BM 14.0741
421 5H2U 1N1 14.2322
422 3FHI ANP 14.2857
423 6CZ3 FLJ 14.3939
424 3P13 RIP 14.5833
425 5Y80 IRE 14.8649
426 4Q5H ANP 14.9425
427 5VNF VAL THR SER VAL VAL 15.2866
428 4C2W ANP 15.3846
429 3KMW ATP 16.2791
430 4BTK DTQ 17.5074
431 3O0G 3O0 18.1208
432 4C2V YJA 18.1818
433 4NFN 2KC 19.0939
434 5TO8 7FM 20.2128
435 3E5A VX6 20.4545
436 4NM5 ADP 20.8333
437 4Y8D 49J 22.1429
438 5LXM ADP 23.6842
439 4PZ6 GMP 23.8095
440 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 25.9259
441 1UNH IXM 26.4423
442 1O9U ADZ 27.7778
443 3BU5 ATP 40
Pocket No.: 2; Query (leader) PDB : 5EQY; Ligand: 5RA; Similar sites found with APoc: 17
This union binding pocket(no: 2) in the query (biounit: 5eqy.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 4OWK NGA None
2 3K5I AIR 1.74564
3 3ACL 3F1 2.36486
4 2OO8 RAJ 2.52366
5 4GNC ASO 2.67559
6 1IOW PHY 3.26797
7 3ZS7 ATP 4
8 5OPM DTP 4.1841
9 3UG4 AHR 4.48878
10 5EXK 5AD 5.43807
11 1CBK ROI 5.625
12 3KO0 TFP 5.94059
13 2VQ5 HBA 7.46269
14 3NV3 GAL NAG MAN 9.42029
15 4F4P 0SB 11.3553
16 4TWP AXI 12.1771
17 5NLD LBT 12.9496
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