Receptor
PDB id Resolution Class Description Source Keywords
3KJD 1.95 Å EC: 2.4.2.30 HUMAN POLY(ADP-RIBOSE) POLYMERASE 2, CATALYTIC FRAGMENT IN C WITH AN INHIBITOR ABT-888 HOMO SAPIENS TRANSFERASE ENZYME-INHIBITOR COMPLEX CATALYTIC FRAGMENT SGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC GLYCOSYLTRANNAD NUCLEUS DNA-BINDING
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEX WITH PARP INHIBITOR ABT-888. BIOCHEMISTRY V. 49 1056 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
78P A:1;
B:1;
Valid;
Valid;
none;
none;
Kd = 2.9 nM
244.292 C13 H16 N4 O C[C@@...
GOL A:580;
B:2;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KJD 1.95 Å EC: 2.4.2.30 HUMAN POLY(ADP-RIBOSE) POLYMERASE 2, CATALYTIC FRAGMENT IN C WITH AN INHIBITOR ABT-888 HOMO SAPIENS TRANSFERASE ENZYME-INHIBITOR COMPLEX CATALYTIC FRAGMENT SGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC GLYCOSYLTRANNAD NUCLEUS DNA-BINDING
Ref.: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COMPLEX WITH PARP INHIBITOR ABT-888. BIOCHEMISTRY V. 49 1056 2010
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
2 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
3 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
4 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
5 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
6 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
2 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
3 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
4 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
5 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
6 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5XSU Kd = 180 nM 8E3 C15 H13 F N4 O2 c1c(cc2c(c....
2 4R6E ic50 = 132 nM 3JD C19 H20 N4 O c1cc2cn(nc....
3 4ZZZ Kd = 0.087 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
4 5XSR Kd = 0.000000064 M 8EC C15 H13 F N4 O S c1c(cc2c(c....
5 6VKK - RPB C19 H18 F N3 O CNCc1ccc(c....
6 3GJW Ki = 0.005 uM GJW C16 H17 N3 O c1cc2n(c1)....
7 4L6S Kd = 0.003 uM 1WQ C21 H21 Cl N2 O2 C[C@H]1C(=....
8 4HHY ic50 = 1.92 nM 15R C33 H30 F N5 O4 c1ccc2c(c1....
9 4UND - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
10 5XST ic50 = 27 nM 8E6 C15 H13 F N4 O S c1c(cc2c(c....
11 3L3L Ki = 33 nM L3L C14 H17 N3 O2 c1cc2c(c(c....
12 4PJT ic50 = 0.57 nM 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
13 3L3M Ki = 0.006 uM A92 C19 H19 F N4 O c1cc(c2c(c....
14 6XVW - O3H C19 H21 N5 O S c1ccc2c(c1....
15 4TVJ ic50 = 251 nM 09L C24 H23 F N4 O3 c1ccc2c(c1....
16 4ZZY Kd = 1.389 uM D7N C20 H24 F3 N3 O2 c1c(cc(c2c....
17 4PJV - 2YQ C19 H14 F2 N6 O Cn1c(ncn1)....
18 3KCZ - 3AB C7 H8 N2 O c1cc(cc(c1....
19 3KJD Kd = 2.9 nM 78P C13 H16 N4 O C[C@@]1(CC....
20 4ZZX Kd = 0.125 uM FSU C13 H16 N2 O3 COCCCN1Cc2....
21 3C4H Kd = 2 uM DRL C8 H10 N2 O S CC1=NC2=C(....
22 4L7P - M95 C20 H19 N3 O3 c1ccc(cc1)....
23 4L7L - 1VA C20 H21 N3 O3 c1ccc(cc1)....
24 4L7N - 1VB C19 H20 N4 O4 S C[C@@H](c1....
25 4L7R - M00 C15 H19 N3 O3 CC[C@@H](C....
26 4L6Z - 1DC C18 H18 N4 O2 C[C@@H](c1....
27 3FHB Kd > 2 uM GAB C7 H7 N O2 c1cc(cc(c1....
28 4L70 - 1V9 C20 H21 N3 O2 CC[C@@H](c....
29 4GV4 ic50 = 0.89 uM MEJ C19 H19 N3 O2 C[C@@H](c1....
30 4GV0 ic50 = 1.3 uM 8ME C18 H18 N4 O2 C[C@@H](c1....
31 4L7O - 1VD C22 H21 N5 O2 C[C@@H](c1....
32 4GV2 - 5ME C18 H18 N4 O2 C[C@H](c1c....
33 6NRG ic50 = 56 nM KYY C17 H12 F N5 O3 c1cc2c(c(o....
34 6NRJ ic50 = 36 nM KYJ C26 H20 N4 O4 c1ccc2c(c1....
35 6NRI ic50 = 27 nM KYM C25 H21 N5 O4 c1cc2c(c(c....
36 6NTU - GLC FRU n/a n/a
37 6NRF ic50 = 18 nM KYV C28 H25 N5 O4 c1ccc2c(c1....
38 6NRH ic50 = 55 nM KYP C25 H23 N5 O4 c1cc2c(c(o....
39 6BHV Kd = 5.87 uM DQV C22 H28 N6 O14 P2 c1cc(cc(c1....
40 2PAX ic50 = 0.18 uM 4AN C12 H8 N2 O2 c1cc2c(ccc....
41 3PAX ic50 = 10 uM 3MB C8 H9 N O2 COc1cccc(c....
42 1EFY Ki = 6 nM BZC C15 H13 N3 O2 COc1cccc(c....
43 1PAX - DHQ C10 H11 N O Cc1cccc2c1....
44 6I8T - H7Z C21 H29 N3 O2 C[C@@H]1c2....
45 6I8M - H7W C21 H29 N3 O2 C[C@H]1c2c....
46 1A26 - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 78P; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 78P 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 78P; Similar ligands found: 420
No: Ligand Similarity coefficient
1 L3L 0.9392
2 HA6 0.9312
3 Q5M 0.9259
4 UN4 0.9217
5 7I2 0.9210
6 IL5 0.9178
7 ELH 0.9151
8 FSU 0.9134
9 MBP 0.9123
10 GZV 0.9122
11 CMG 0.9106
12 5JT 0.9092
13 5WT 0.9090
14 YEX 0.9080
15 H35 0.9077
16 6TJ 0.9077
17 ZYV 0.9076
18 QUB 0.9074
19 NU3 0.9073
20 5WS 0.9067
21 MUX 0.9063
22 M01 0.9060
23 56N 0.9054
24 KMP 0.9050
25 KWB 0.9049
26 57D 0.9044
27 KLV 0.9044
28 3Y7 0.9044
29 HHV 0.9043
30 5P3 0.9037
31 PJK 0.9033
32 531 0.9031
33 5NN 0.9028
34 3WN 0.9028
35 3WO 0.9028
36 SG2 0.9026
37 XFE 0.9025
38 OSB 0.9025
39 ZEA 0.9019
40 H4B 0.9017
41 CUT 0.9016
42 NAR 0.9015
43 DXK 0.9012
44 7NU 0.9011
45 EMU 0.9011
46 AGI 0.9002
47 AZY 0.8992
48 EYM 0.8991
49 3WK 0.8988
50 NTF 0.8986
51 FF2 0.8984
52 6ZW 0.8983
53 0SY 0.8983
54 WLH 0.8982
55 YE7 0.8981
56 AC2 0.8976
57 CHQ 0.8972
58 5RM 0.8968
59 0RY 0.8961
60 2GQ 0.8956
61 BIO 0.8950
62 64F 0.8947
63 7L4 0.8945
64 3JC 0.8945
65 NIY 0.8944
66 QMS 0.8943
67 ZME 0.8942
68 X0T 0.8941
69 CX4 0.8936
70 V2Z 0.8935
71 6XC 0.8933
72 67Y 0.8932
73 GA2 0.8928
74 4L2 0.8927
75 0OP 0.8926
76 CDY 0.8926
77 H7S 0.8926
78 FER 0.8925
79 GL6 0.8924
80 JOH 0.8923
81 G6P 0.8921
82 BDI 0.8920
83 1Q4 0.8919
84 8G6 0.8919
85 KFN 0.8918
86 1QV 0.8915
87 4K2 0.8915
88 EXD 0.8915
89 4AB 0.8914
90 QR2 0.8914
91 WUB 0.8913
92 B23 0.8912
93 CR1 0.8911
94 H2B 0.8910
95 HBI 0.8910
96 FUZ 0.8909
97 3AK 0.8909
98 3GX 0.8907
99 F40 0.8907
100 ZRK 0.8907
101 EYA 0.8899
102 B4L 0.8899
103 1X8 0.8895
104 IK1 0.8895
105 ZEZ 0.8894
106 TRP 0.8889
107 GRX 0.8889
108 3WJ 0.8887
109 ALR 0.8886
110 CUH 0.8885
111 ZRL 0.8885
112 M3W 0.8884
113 ET0 0.8882
114 AH9 0.8881
115 P4L 0.8880
116 M02 0.8879
117 4F8 0.8878
118 GMP 0.8877
119 MXD 0.8877
120 774 0.8874
121 RVE 0.8874
122 DBS 0.8873
123 QC1 0.8872
124 GNG 0.8865
125 ZIP 0.8865
126 NFZ 0.8864
127 NIR 0.8862
128 5E4 0.8858
129 LI4 0.8857
130 6NZ 0.8857
131 34L 0.8855
132 5AD 0.8852
133 GO8 0.8852
134 A4V 0.8852
135 KYN 0.8849
136 GNV 0.8849
137 WS7 0.8848
138 FYJ 0.8845
139 3D8 0.8845
140 8HH 0.8841
141 ID8 0.8839
142 JTF 0.8837
143 F5C 0.8837
144 6PB 0.8837
145 55D 0.8837
146 0J4 0.8837
147 RUG 0.8836
148 PLP 0.8835
149 CL9 0.8833
150 B21 0.8833
151 1FL 0.8831
152 C09 0.8830
153 A4G 0.8829
154 AKD 0.8824
155 N88 0.8823
156 P9I 0.8823
157 FY8 0.8823
158 MUR 0.8823
159 VJJ 0.8823
160 AUY 0.8821
161 JP2 0.8821
162 7PJ 0.8817
163 0H5 0.8817
164 BG6 0.8815
165 OX2 0.8815
166 2O6 0.8814
167 D80 0.8813
168 5OF 0.8813
169 S1D 0.8812
170 G1P 0.8812
171 AJD 0.8812
172 2KU 0.8812
173 AH3 0.8811
174 5F8 0.8805
175 3DT 0.8803
176 DFL 0.8803
177 NPA 0.8802
178 C9M 0.8802
179 6J9 0.8802
180 O2Y 0.8800
181 MPP 0.8799
182 6J3 0.8798
183 WA2 0.8796
184 5V7 0.8793
185 X04 0.8793
186 N2M 0.8792
187 VBC 0.8791
188 IQQ 0.8786
189 7A9 0.8784
190 JSX 0.8783
191 KF5 0.8781
192 5B2 0.8781
193 MZM 0.8780
194 64E 0.8779
195 IKY 0.8776
196 YE6 0.8776
197 NEU 0.8774
198 ONZ 0.8773
199 M6P 0.8772
200 C4E 0.8769
201 5KN 0.8769
202 4GU 0.8767
203 Q4G 0.8767
204 0FR 0.8766
205 X8E 0.8765
206 7VF 0.8764
207 GJK 0.8764
208 ZYW 0.8761
209 2LW 0.8760
210 ZSP 0.8760
211 YO5 0.8760
212 HKK 0.8760
213 DE7 0.8760
214 5FL 0.8759
215 SQM 0.8758
216 Q9T 0.8757
217 5E5 0.8755
218 TLF 0.8754
219 LP8 0.8753
220 UKV 0.8752
221 CTE 0.8750
222 L07 0.8748
223 2UD 0.8747
224 BZM 0.8746
225 WG8 0.8745
226 7AP 0.8743
227 GI4 0.8742
228 THM 0.8742
229 XZ8 0.8741
230 MG7 0.8741
231 GI1 0.8741
232 JTA 0.8740
233 9F8 0.8739
234 BGU 0.8738
235 VT3 0.8738
236 2LX 0.8737
237 S7D 0.8735
238 7ZL 0.8735
239 WS6 0.8735
240 4P8 0.8734
241 4R1 0.8733
242 5WM 0.8731
243 TQ1 0.8731
244 0DN 0.8731
245 2JK 0.8730
246 XG1 0.8729
247 0J2 0.8729
248 4GP 0.8729
249 AVA 0.8729
250 CFK 0.8727
251 P83 0.8727
252 JO5 0.8726
253 ER6 0.8723
254 MPU 0.8722
255 CC5 0.8722
256 4UO 0.8720
257 3D1 0.8718
258 6J5 0.8716
259 NPL 0.8716
260 FTU 0.8715
261 XYA 0.8713
262 B2E 0.8713
263 TMC 0.8712
264 HO4 0.8711
265 NWD 0.8709
266 HFT 0.8709
267 MUK 0.8708
268 BZC 0.8708
269 F6P 0.8707
270 YM6 0.8706
271 KCH 0.8705
272 49P 0.8705
273 DDC 0.8705
274 RGG 0.8705
275 25O 0.8705
276 G30 0.8703
277 4FF 0.8701
278 ITE 0.8701
279 5V5 0.8701
280 DT7 0.8700
281 XEZ 0.8700
282 FNA 0.8698
283 XEV 0.8696
284 96Z 0.8694
285 TCW 0.8693
286 AP6 0.8693
287 9E3 0.8692
288 4ZF 0.8692
289 5WN 0.8691
290 3IL 0.8691
291 6DP 0.8690
292 DBQ 0.8688
293 8Y7 0.8687
294 DNQ 0.8687
295 BBY 0.8684
296 X2M 0.8682
297 1HR 0.8682
298 TU0 0.8681
299 PBG 0.8680
300 EKH 0.8679
301 2QU 0.8679
302 EVO 0.8679
303 N7I 0.8679
304 B4O 0.8678
305 8HG 0.8677
306 5F1 0.8675
307 3L1 0.8671
308 GNJ 0.8671
309 5BT 0.8669
310 BOQ 0.8669
311 MIL 0.8669
312 XJ2 0.8669
313 QMR 0.8668
314 9UL 0.8668
315 5I5 0.8668
316 GVI 0.8666
317 9XZ 0.8666
318 L5D 0.8665
319 TQU 0.8664
320 LVY 0.8663
321 CZ0 0.8658
322 LL1 0.8656
323 R9G 0.8656
324 C0W 0.8656
325 47N 0.8653
326 K3Y 0.8652
327 JR2 0.8652
328 2WU 0.8651
329 PIQ 0.8651
330 5TZ 0.8651
331 2T4 0.8651
332 TZM 0.8649
333 ASE 0.8649
334 39Z 0.8648
335 159 0.8647
336 CIY 0.8645
337 28S 0.8645
338 SGV 0.8642
339 5P7 0.8641
340 HWH 0.8641
341 SU9 0.8640
342 FHI 0.8636
343 PXP 0.8634
344 2JX 0.8634
345 5GT 0.8634
346 4VT 0.8633
347 3AD 0.8633
348 9GP 0.8633
349 BHS 0.8632
350 6HP 0.8632
351 I7A 0.8632
352 0DF 0.8631
353 MFR 0.8630
354 I2E 0.8627
355 5WK 0.8627
356 S98 0.8626
357 92O 0.8626
358 5F5 0.8626
359 BJ4 0.8625
360 IOS 0.8624
361 CC6 0.8623
362 NIF 0.8622
363 LU2 0.8621
364 ADN 0.8621
365 IBM 0.8619
366 5E1 0.8619
367 DTR 0.8614
368 LLT 0.8613
369 22T 0.8613
370 D87 0.8612
371 II4 0.8607
372 FC2 0.8606
373 M9N 0.8605
374 W8G 0.8605
375 8DA 0.8605
376 FNT 0.8604
377 FT6 0.8603
378 7D7 0.8603
379 AOJ 0.8599
380 QZ8 0.8599
381 K68 0.8596
382 9RM 0.8593
383 EGR 0.8590
384 FCW 0.8585
385 2L2 0.8584
386 I7B 0.8583
387 5FD 0.8581
388 4NO 0.8581
389 DTE 0.8578
390 2V0 0.8576
391 B61 0.8573
392 BVD 0.8573
393 5XL 0.8566
394 EWG 0.8564
395 U14 0.8563
396 B86 0.8562
397 BB4 0.8559
398 0GA 0.8557
399 DK1 0.8557
400 EMF 0.8556
401 7M2 0.8552
402 Q2R 0.8551
403 I7C 0.8551
404 APS 0.8549
405 BNY 0.8548
406 ABJ 0.8548
407 JNW 0.8544
408 ZHA 0.8544
409 XIF XYP 0.8542
410 NOS 0.8541
411 UN9 0.8540
412 DT9 0.8535
413 HMD 0.8531
414 XTS 0.8526
415 ROL 0.8522
416 JVD 0.8521
417 4Z9 0.8519
418 0SX 0.8517
419 6QF 0.8517
420 2NJ 0.8504
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KJD; Ligand: 78P; 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: 3kjd.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3KJD; Ligand: 78P; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 3kjd.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3ESS 18N 4.78261
2 6W65 T9D 16.9675
3 6W65 T9D 16.9675
APoc FAQ
Feedback