Receptor
PDB id Resolution Class Description Source Keywords
5A5Q 1.97 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 3-METHYL-8-PIPERIDIN-4-YLAMINO-1,2-DIHYDRO-1,7- N APHTHYRIDIN-2-ONE HYDROCHLORIDE HOMO SAPIENS HYDROLASE INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPAFAMILY AAA DOMAIN-CONTAINING PROTEIN 2
Ref.: FRAGMENT-BASED DISCOVERY OF LOW-MICROMOLAR ATAD2 BROMODOMAIN INHIBITORS. J.MED.CHEM. V. 58 5649 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:2109;
A:2110;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
6XC A:2111;
 Valid;
 none;
 Kd = 21 uM
258.319 C14 H18 N4 O CC1=C...
SO4 A:2112;
A:2113;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HDN 1.9 Å EC: 3.6.1.3 CRYSTAL STRUCTURE OF HUMAN ATAD2 BROMODOMAIN IN COMPLEX WITH 8-((8-METHYL-8-AZABICYCLOOCTAN-3-YL)AMINO)-1,7-NAPHTHYRIDIN HOMO SAPIENS INHIBITOR ATAD2 BROMODOMAIN EPIGENETICS ATPASE FAMILY AACONTAINING PROTEIN 2 TRANSCRIPTION
Ref.: AIMING TO MISS A MOVING TARGET: BROMO AND EXTRA TER DOMAIN (BET) SELECTIVITY IN CONSTRAINED ATAD2 INHIB J. MED. CHEM. V. 61 8321 2018
Members (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
19 6VEO - YD4 C26 H33 N5 O4 S Cc1cc(cnc1....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5A5R ic50 = 1.3 uM NP8 C20 H23 N5 O2 CC1=Cc2c(c....
2 5A82 ic50 = 2.51 uM YEJ C20 H28 N4 O4 S CC1=Cc2ccn....
3 5A5Q Kd = 21 uM 6XC C14 H18 N4 O CC1=Cc2ccn....
4 6S55 - KW5 C17 H21 Br N4 O5 S C[C@H]1CCC....
5 5A81 Kd = 2.9 uM 78J C21 H30 N4 O2 CC1=Cc2ccn....
6 5A5P ic50 = 0.1 mM JTF C14 H19 N3 O CC1=Cc2ccc....
7 4TU4 Kd = 175 uM 37N C18 H16 N2 O5 S Cc1c(c(on1....
8 4TZ8 Kd = 500 uM 39U C9 H13 N3 O S CC1(Cc2c(s....
9 5A5O - J5I C10 H9 N O CC1=Cc2ccc....
10 6HDN ic50 = 3.16 uM FZB C17 H22 N4 O CC1=Cc2ccn....
11 6S57 - KVT C20 H28 N4 O5 S Cc1ccc(cc1....
12 5A5N - 8WS C11 H21 N3 O3 CC(=O)NCCC....
13 4TTE Kd = 202 uM 36Z C13 H14 N2 O3 Cc1c(c(on1....
14 4TYL Kd = 600 uM 39O C10 H13 N3 O Cc1cc2c(cc....
15 4TZ2 Kd = 350 uM 39R C14 H12 N4 c1ccc(cc1)....
16 5A83 ic50 = 0.158 uM YD3 C27 H34 N4 O4 S Cc1cc(cnc1....
17 5LJ0 ic50 = 0.00000001 M 6XX C28 H35 F2 N5 O3 Cc1cc(cnc1....
18 6S56 - KVZ C22 H23 Cl N4 O5 S CN(C)S(=O)....
19 6VEO - YD4 C26 H33 N5 O4 S Cc1cc(cnc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6XC; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 6XC 1 1
2 FZB 0.623188 0.703125
3 YEJ 0.511628 0.684211
4 78J 0.5 0.866667
5 NP8 0.404494 0.83871
Similar Ligands (3D)
Ligand no: 1; Ligand: 6XC; Similar ligands found: 479
No: Ligand Similarity coefficient
1 3WL 0.9501
2 FNA 0.9498
3 1Q4 0.9478
4 3GX 0.9470
5 DTQ 0.9457
6 TQ3 0.9439
7 XZ1 0.9423
8 JTF 0.9415
9 6JO 0.9407
10 3AK 0.9407
11 6JM 0.9360
12 6QT 0.9336
13 1V4 0.9329
14 1V3 0.9316
15 5NN 0.9305
16 0H5 0.9301
17 HA6 0.9297
18 E9L 0.9296
19 7L4 0.9294
20 6DQ 0.9286
21 KMP 0.9283
22 3WK 0.9270
23 3TI 0.9260
24 LI4 0.9258
25 NKI 0.9258
26 FL8 0.9256
27 B4L 0.9251
28 1HP 0.9250
29 FSE 0.9244
30 M3W 0.9243
31 57D 0.9232
32 7M5 0.9230
33 DDC 0.9221
34 40N 0.9220
35 7M2 0.9217
36 3JC 0.9216
37 BC3 0.9207
38 AGI 0.9204
39 SNJ 0.9203
40 O9Q 0.9196
41 DX2 0.9196
42 UI2 0.9192
43 H2W 0.9190
44 0DF 0.9190
45 I0D 0.9185
46 NYJ 0.9182
47 W8L 0.9181
48 ASE 0.9180
49 TQ4 0.9179
50 QUB 0.9178
51 3WN 0.9177
52 3WO 0.9177
53 CDJ 0.9175
54 2QU 0.9173
55 8RK 0.9164
56 6NJ 0.9163
57 IM4 0.9162
58 DFV 0.9160
59 VT3 0.9158
60 C09 0.9155
61 PIQ 0.9154
62 DFL 0.9154
63 BJ4 0.9152
64 5B2 0.9151
65 YE7 0.9144
66 O9Z 0.9141
67 7VF 0.9140
68 NAR 0.9138
69 4YF 0.9137
70 6BK 0.9135
71 108 0.9134
72 QUE 0.9129
73 9CE 0.9125
74 BHF 0.9125
75 34L 0.9124
76 UNM 0.9123
77 338 0.9121
78 O9T 0.9120
79 4JV 0.9120
80 S0I 0.9116
81 BIE 0.9112
82 D64 0.9109
83 MQ1 0.9107
84 AP6 0.9107
85 P4L 0.9105
86 HH6 0.9105
87 F40 0.9103
88 PZB 0.9103
89 BRY 0.9098
90 JHY 0.9096
91 QS4 0.9095
92 D87 0.9090
93 96Z 0.9088
94 DXK 0.9087
95 2NJ 0.9085
96 74Z 0.9084
97 F91 0.9081
98 CHV 0.9081
99 IDZ 0.9081
100 H0V 0.9079
101 LQG 0.9077
102 SNB 0.9070
103 LWS 0.9069
104 SGW 0.9069
105 WLH 0.9069
106 20D 0.9067
107 0SX 0.9065
108 1V8 0.9062
109 U14 0.9062
110 1V1 0.9061
111 VJJ 0.9059
112 Q5M 0.9057
113 LU2 0.9056
114 SU9 0.9055
115 DH2 0.9055
116 FX5 0.9054
117 EYM 0.9050
118 CX4 0.9048
119 T34 0.9047
120 A63 0.9046
121 HUL 0.9046
122 C4E 0.9044
123 7LU 0.9038
124 2GQ 0.9038
125 22T 0.9036
126 CU5 0.9036
127 5P3 0.9033
128 HWH 0.9026
129 2H4 0.9025
130 1CE 0.9025
131 EVO 0.9024
132 NIF 0.9020
133 3F4 0.9020
134 Q4G 0.9017
135 NAL 0.9017
136 EYA 0.9015
137 LIG 0.9010
138 9XZ 0.9009
139 8HG 0.9002
140 58N 0.8997
141 25F 0.8996
142 ET0 0.8993
143 SZ5 0.8991
144 2BI 0.8991
145 2T4 0.8989
146 SAK 0.8988
147 5E5 0.8986
148 4K2 0.8985
149 5V7 0.8985
150 5WW 0.8984
151 3SU 0.8980
152 SCE 0.8980
153 NW1 0.8980
154 XG1 0.8976
155 A73 0.8974
156 CWE 0.8973
157 RGK 0.8973
158 MYC 0.8972
159 5ZM 0.8968
160 EV2 0.8967
161 RK4 0.8967
162 X2M 0.8965
163 ER6 0.8964
164 DQH 0.8963
165 1HR 0.8961
166 DE7 0.8961
167 3QI 0.8961
168 ML1 0.8961
169 CU8 0.8958
170 XEV 0.8958
171 L07 0.8952
172 MRI 0.8951
173 0OK 0.8950
174 1FL 0.8950
175 4EU 0.8947
176 IQQ 0.8947
177 12R 0.8946
178 YZ9 0.8946
179 LP8 0.8944
180 YM6 0.8943
181 U4J 0.8943
182 52F 0.8943
183 MYU 0.8942
184 5P7 0.8939
185 T61 0.8939
186 QUG 0.8939
187 BXZ 0.8938
188 J8G 0.8935
189 B7H 0.8934
190 BZM 0.8933
191 78P 0.8933
192 CC6 0.8932
193 XYP XIM 0.8930
194 272 0.8930
195 5PK 0.8930
196 UN4 0.8928
197 6B5 0.8927
198 CMG 0.8927
199 AJD 0.8926
200 NWD 0.8925
201 KOM 0.8925
202 L3L 0.8924
203 LI7 0.8923
204 AKD 0.8923
205 AXX 0.8921
206 EMU 0.8921
207 NU3 0.8921
208 FHI 0.8917
209 MBP 0.8917
210 WST 0.8916
211 H35 0.8914
212 D80 0.8914
213 AJ4 0.8913
214 EY7 0.8911
215 3D8 0.8909
216 9F8 0.8908
217 EXG 0.8907
218 7EH 0.8906
219 PE2 0.8906
220 FY8 0.8905
221 RC0 0.8903
222 P9I 0.8902
223 B5A 0.8902
224 KTM 0.8902
225 YEX 0.8900
226 91F 0.8900
227 FUN 0.8898
228 Q0K 0.8897
229 2UD 0.8895
230 TRP 0.8894
231 AUE 0.8893
232 QEI 0.8891
233 XJ2 0.8887
234 RFZ 0.8883
235 IOP 0.8883
236 KWB 0.8881
237 L5D 0.8880
238 AVA 0.8879
239 7CS 0.8879
240 08C 0.8877
241 5E2 0.8872
242 658 0.8872
243 GA2 0.8871
244 FT6 0.8871
245 4NR 0.8870
246 3WJ 0.8864
247 TOP 0.8862
248 R4E 0.8862
249 531 0.8860
250 IRH 0.8859
251 MQS 0.8859
252 LVY 0.8858
253 RDL 0.8858
254 I0G 0.8856
255 IQW 0.8855
256 3RH 0.8854
257 DX7 0.8850
258 IK1 0.8850
259 AUG 0.8848
260 5KN 0.8848
261 FCW 0.8847
262 4RG 0.8846
263 FVY 0.8845
264 3CA 0.8845
265 56N 0.8843
266 PMM 0.8841
267 ML2 0.8841
268 Q8D 0.8839
269 5FL 0.8839
270 BB4 0.8836
271 KXN 0.8835
272 6QX 0.8834
273 MN QAY 0.8834
274 FYJ 0.8832
275 Q8G 0.8830
276 AIQ 0.8829
277 KWQ 0.8829
278 JFS 0.8827
279 LLG 0.8822
280 JSX 0.8820
281 28S 0.8816
282 9JT 0.8815
283 MW5 0.8814
284 6FX 0.8810
285 ZRL 0.8810
286 IXM 0.8809
287 018 0.8808
288 GQZ 0.8807
289 5F8 0.8807
290 39Z 0.8806
291 BL7 0.8806
292 4YE 0.8806
293 UV4 0.8804
294 HAN 0.8804
295 AC2 0.8804
296 A4V 0.8804
297 69W 0.8802
298 EV3 0.8801
299 3DE 0.8801
300 NVS 0.8801
301 4L2 0.8800
302 BUX 0.8799
303 HWB 0.8797
304 0MB 0.8789
305 MT6 0.8787
306 MHB 0.8787
307 VM1 0.8782
308 5WN 0.8782
309 7NU 0.8781
310 0UL 0.8780
311 C0Y 0.8779
312 3EB 0.8776
313 JYE 0.8772
314 H7S 0.8772
315 8EQ 0.8772
316 ZAR 0.8770
317 RKY 0.8769
318 OTA 0.8769
319 8BD 0.8768
320 21E 0.8767
321 JAK 0.8766
322 32V 0.8765
323 PNX 0.8765
324 49P 0.8765
325 5DN 0.8764
326 WUL 0.8762
327 4RV 0.8760
328 BIT 0.8759
329 X0T 0.8758
330 GUS 0.8756
331 NXB 0.8754
332 D5F 0.8754
333 2LX 0.8753
334 7G1 0.8752
335 DYZ 0.8752
336 ZEA 0.8752
337 GEN 0.8751
338 AZY 0.8750
339 2JX 0.8750
340 NIY 0.8750
341 4GU 0.8749
342 27F 0.8748
343 HMZ 0.8747
344 6BD 0.8746
345 VGG 0.8745
346 RVE 0.8745
347 4ZF 0.8745
348 II4 0.8744
349 WA2 0.8744
350 NPZ 0.8743
351 E6Q 0.8741
352 1UZ 0.8741
353 6JP 0.8740
354 9BF 0.8739
355 ZIP 0.8738
356 MIL 0.8735
357 2GE 0.8734
358 GNG 0.8734
359 TVZ 0.8733
360 RSV 0.8732
361 3IL 0.8731
362 KTV 0.8727
363 AX1 0.8723
364 S1D 0.8722
365 UN3 0.8721
366 IDD 0.8720
367 O2Q 0.8719
368 T5J 0.8716
369 OA4 0.8715
370 ELH 0.8715
371 M9N 0.8715
372 0OM 0.8713
373 X29 0.8711
374 4Z9 0.8710
375 IM5 0.8709
376 A0O 0.8705
377 WDW 0.8701
378 2QV 0.8701
379 JBB 0.8700
380 28A 0.8700
381 5WM 0.8700
382 J8D 0.8699
383 AVX 0.8698
384 KP2 0.8698
385 K8W 0.8698
386 3IB 0.8697
387 OPA 0.8696
388 GMP 0.8695
389 8HH 0.8693
390 FNT 0.8692
391 PP1 0.8692
392 LM7 0.8688
393 A64 0.8688
394 ZEZ 0.8688
395 7FC 0.8685
396 2XY 0.8684
397 0QV 0.8683
398 5DE 0.8682
399 BN1 0.8682
400 5WS 0.8681
401 3B4 0.8674
402 B61 0.8674
403 8Y7 0.8670
404 9ME 0.8664
405 4P8 0.8664
406 GI4 0.8664
407 FVV 0.8663
408 1SF 0.8659
409 LRW 0.8658
410 AUV 0.8658
411 HKK 0.8657
412 TYP 0.8657
413 AJ6 0.8654
414 OAI 0.8649
415 OJ7 0.8647
416 2L1 0.8645
417 NQ7 0.8645
418 6KP 0.8645
419 TI7 0.8645
420 AIR 0.8645
421 TCR 0.8643
422 555 0.8643
423 LL1 0.8643
424 TQ1 0.8642
425 020 0.8641
426 PZX 0.8640
427 GOW 0.8640
428 TGW 0.8638
429 MEX 0.8636
430 ISX 0.8636
431 5R9 0.8635
432 3G1 0.8635
433 27K 0.8627
434 6TJ 0.8627
435 JVD 0.8623
436 0RU 0.8623
437 Y70 0.8620
438 Q9G 0.8620
439 340 0.8619
440 XYP XYP 0.8619
441 5SB 0.8614
442 PP2 0.8612
443 AB3 0.8612
444 H4B 0.8611
445 76P 0.8610
446 C0W 0.8610
447 8M5 0.8608
448 5EZ 0.8607
449 UX0 0.8605
450 6WU 0.8603
451 OUA 0.8603
452 53X 0.8602
453 YJX 0.8601
454 IEO 0.8600
455 IMK 0.8599
456 5XM 0.8598
457 JNW 0.8598
458 EY2 0.8596
459 MG7 0.8594
460 ZJB 0.8588
461 DIH 0.8586
462 CL9 0.8584
463 P34 0.8582
464 QW5 0.8582
465 43O 0.8577
466 LTN 0.8576
467 CDY 0.8555
468 15Q 0.8555
469 0OP 0.8549
470 JXT 0.8544
471 6DE 0.8542
472 PFT 0.8541
473 5UX 0.8540
474 XYS XYS 0.8537
475 JYW 0.8532
476 GT2 0.8524
477 IPJ 0.8524
478 GJB 0.8523
479 5WK 0.8509
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6HDN; Ligand: FZB; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 6hdn.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4XUB 43D 27.3504
2 6HAZ FX5 27.6423
3 6HAZ FX5 27.6423
4 6DF7 G9V 30.7692
5 6DF7 G9V 30.7692
6 6J3O B4L 30.7692
7 6J3P B8O 39.2308
8 6J3P B8O 39.2308
9 5MG2 7M8 40
10 5IGL BMF 46.9231
11 5MLJ 9ST 50
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